Because of Thunder's higher power.
In Ubers, half the Pokémon have 100+ HP and Defenses, and Thunderbolt without STAB in Ubers is like hitting a Chansey with Earth Power, ain't gonna hit so hard.
Thunder trades accuracy for the extra power, and in Ubers, sorry mate, but you would have to take the nice risk.
Thunder turns some 2HKO's by Thunderbolt to OHKO's, 3HKO's to 2HKO's, and so on.
A few calcs:
+2 252+ SpA Xerneas Thunder vs. 0 HP / 0 SpD Kyogre-Primal: 352-416 (103.2 - 121.9%) -- guaranteed OHKO
+2 252+ SpA Xerneas Thunderbolt vs. 0 HP / 0 SpD Kyogre-Primal: 288-340 (84.4 - 99.7%) -- guaranteed 2HKO
+2 252+ SpA Xerneas Thunder vs. 252 HP / 0 SpD Arceus-Water: 452-534 (101.8 - 120.2%) -- guaranteed OHKO
+2 252+ SpA Xerneas Thunderbolt vs. 252 HP / 0 SpD Arceus-Water: 372-438 (83.7 - 98.6%) -- guaranteed 2HKO
There are a lot more calcs like this, this just showcases that in Ubers, need for higher power is req.
So yep, you have to take the risk if you wanna win.
(btw take this answer as NDAG...)
This is for yours and swastiks answers btw since they both have calcs :P
While thunder may work effectively to take ohkos or abuse kyogre rain, what about lower tiers? Take my boy thundurus for example
252 SpA Thundurus Thunderbolt vs. 0 HP / 0 SpD Primarina: 254-300 (84.3 - 99.6%) -- guaranteed 2HKO
252 SpA Thundurus Thunder vs. 0 HP / 0 SpD Primarina: 308-366 (102.3 - 121.5%) -- guaranteed OHKO
Sure this is niche and Primarina would be switching into other attacks becausw of its good typing, and also rain isnt too common, but still. Id expect thunder to be on at least one other smogon set, but it Doesnt appear to be(besides galvantula, who has compound eyes so it Doesnt really count)
Ik this is hard to answers but can anyone find a more specific reason not for its ubers use, but its non rain team low tier no use?
If not thats fine but :P
I guess you want to know why Thunder ain't used, and they recommend TBolt.
The main reason for this is, that Thunderbolt is gonna nail all the foes in lower tiers, with a nice amount of them having only 85+ Defenses, and Thunder's low accuracy is too much to gamble with. If it misses, ggswp, if it doesn't still ggswp, but on Thunderbolt, let's take Primarina for example, after Rocks damage, it has a nice chance to KO (252 SpA Thundurus Thunderbolt vs. 0 HP / 4 SpD Primarina: 254-300 (84.3 - 99.6%) -- 81.3% chance to OHKO after Stealth Rock). Thunderbolt's nice BP of 90 is nice for low tiers (Oh I used nice two times).
Another thing is, Thundurus gets STAB from TBolt, whereas things like Xern don't get the STAB factor on Bolt.
From a The Smog Article, I'll quote:
Thunderbolt, in general, is a good move. In OU and below, Thunderbolt suffices as a good coverage move. However, in Ubers, where most Pokémon have 100/100 in their specially defensive stats, without STAB, even super effective Thunderbolts are tickling common Ubers. For example, Choice Scarf Genesect only does 36.14% - 43.07% to max HP Kyogre with Thunderbolt, which is only a 3HKO. Now, I know that people hate Thunder and its accuracy, but in Ubers, you NEED that power, and that 70% accuracy is just something you're going to have to accept and take a gamble on. Even then, it's not always a gamble, since with Kyogre in Ubers being like Rafael Nadal on clay courts, Thunder is the best choice overall.
I did note that there were a couple of exceptions to this rule. Basically, just like Ice Beam, anything with STAB on Thunderbolt are perfectly fine to use the move, since they have enough power on it. This would include the Thundurus formes, Electric Arceus, and to a certain extent, Magnezone. Another Pokémon that can also be accepted to use Thunderbolt is Fire Arceus. Even in Fire Arceus's case, it is a huge toss up between Thunderbolt and Thunder. It uses Thunderbolt because it requires the coverage in the sun to strike down Ho-Oh, although Thunder would allow it to defeat Kyogre more efficiently. In any case, it is generally accepted that Fire Arceus can use Thunderbolt because it is a designated sun sweeper. This does not mean you can extend this to say, Palkia in a sun team, because Palkia's main purpose is to check Kyogre, which would bring rain along, making Thunder the ideal choice.
The Article was of Gen 5, but I guess the same rule would apply here also.
Hope it helped!!