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Do different save files have different shiny rates because of ID/Secret IDs?

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I'm just curious if this could be true. Secret IDs impact the generation of specific things in older games and are the basis of the Cute Charm glitch. I'm wondering if Secret IDs can help normal shiny hunting or not. I seem to have a way easier time finding shinies in one of my games than any of my others. Also are Secret IDs in all Pokemon games?

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what's a secret id
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The Cute Charm error is caused by a limited range of possible PIDs when the ability activates, not the TID or SID directly.
There is an oversight with Shiny odds in BD/SP caused by a poor implementation of RNG for generating PIDs https://twitter.com/SciresM/status/1461396140734124033 , but in general, every TID/SID is as good as any other (or very very close to it). I may get around to writing an answer explaining why.

And yes SIDs are in every game since Gen 3. In Gen 6+, you will sometimes hear about a "TSV" (short for Trainer Shiny Value), but that's just a function of the TID and SID.
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I know Emerald save files effectively have different shiny rates because the seeds are weird in that game. GSC and FRLG might have similar mechanics, but I don't know as much about those games.
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From what I understand, the way it works is that the game gives you a SID at the start. Every Pokemon has    a PID, and if the PID matches the SID, then it's a shiny. So, unless there's a glitch in the way that it calculates the PID, every SID is just as good as the next one.
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How do you know the PRNG doesn't affect the shiny chance in weird ways? A lot of those mechanics arguably don't count as glitches.
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Because I watch a lot of rng manipulation on YouTube (specifically guaranteed shiny rng for gen 3)  and I know that it works in a very predictable manner, especially since you specified the older games, which in my mind is all the games before X&Y. However, RNG manips work in every game, it just gets harder because of seed generation.
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Re:  Are secret ids in all games?
From gens 4-7, I know are yes. Unsure about 1-3 and 8-9

Edit: just realize fizz commented on that already lol
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And none of the Trainer IDs or SIDs are better or worse for RNG abuse? At least I know that some IDs allow early shiny frames in Emerald.
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No. The way it works is that each frame the game runs a calculation based on the Seed that it generated. The personal ID (PID) and secret ID (SID) are just how the game determines if a Pokemon is a shiny. The PID is calculated by the trainer ID (TID) and the PID is calculated by the seed. That means that some shinys will spawn earlier simply because that's when the two calculations match. So yes, If you're trying to speed run, or in this case, shiny hunt, then some SID are better for one or two Pokemon, but that's about it. There is no definitive best SID because each Pokemon has there own PID that is determined by the seed, which in most of the older games, can be set to a specific value. So depending on the Pokemon you want to be shiny, your'e either going to have a good SID or a bad SID, but that same SID could be really good for a different Pokemon.
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By "different Pokemon", do you mean different species? As far as I know, the game ignores species when generating PIDs/personalities, and the shiny formula also doesn't depend on species. I think different TIDs and SIDs are good for different methods (method 1, method 2, etc.), but that's just about it.
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No, I mean different Pokemon. Each frame, the seed runs a calculation which determines the species, IVs, EVs, Personality, etc if you were to encounter a Pokemon on that frame. It also calculates the PID during that time as well.
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Pokemon are not Shiny when their PID matches the SID. All three of the TID, SID, and PID are involved in computing shinys. There is the "TSV" (a function of the TID and SID) that can predict shinys when compared to the PID, but the SID alone can't do that.
Also, I wouldn't attempt to answer this question using only Gen 3 RNG. I linked an example above where some TSVs are better than others in BD/SP, which would suffice as an accurate (but not comprehensive) answer to this question.

BTW this sentence doesn't make sense: "The PID is calculated by the trainer ID (TID) and the PID is calculated by the seed." Which Gen 3 game are you talking about?
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First off, I am using my knowledge of Emerald, and second off, I meant to say the SID is calculated by the TID.
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That makes sense. Though onlookers should know a couple extra things:
1. Precisely what happens is the game sets the TID to the initial seed and calculates the SID afterward using the same seed, which means the SID is inextricably linked to the TID (and maybe "calculate" is the wrong term).
2. This is not implemented the same way in other Gen 3 games, and it is implemented completely differently in other generations.
3. I'm being pedantic and this doesn't mean a great deal for the answer to this question.
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Fizz, do you think this answer correctly answers the question? Personally, I don't really understand the answer, especially with all of the explanation for it in the comments below. I want to convert it to a comment.
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I say go ahead. The Dworks person isn't defending this answer anymore.
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It's correct insofar as every TSV is as good as any other in the majority of cases. But its reasoning is inaccurate and it ignores edge cases (which there may be more of -- I don't know how the RNG is implemented in every Pokemon game).
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1 Answer

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Statistically speaking no, especially when ignoring specific cases like RNG Manipulation (certain shiny + IV combos are only possible on certain TID + SID combos, more notably when not breeding), or the Cute Charm bug. The number of PIDs that are shiny are always the same per save file given how the shininess calculation goes.

source

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Out of interest, what authority does the typical Smogon user on that thread have on these subjects which we don't? I gave an example of when TID/SID *does* impact Shiny chance from a reputable source, which was not mentioned there.
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That user's answers although obviously very literate seem not entirely decisive and/or conclusive. Not doubting their knowledge on this topic, but their answer of "Depends on hunting method" when referring to PokeRadar chaining in DPPt or BDSP is suspect, at least to me.

Also they give no data to back their claims up, although I know that's not a requirement on Smogon, and accept that easily.
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There's a reason why I pasted this answer and none of the other answers onto Pokebase.
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I will take this to be true however incomplete for the reasons Fizz stated
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Someone on Smogon just said BDSP is the only core series game with inconsistencies like that. All other core series games have the exact same number of shiny PIDs in each save file.
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