I don’t fully understand the question, but what I think you’re asking is about hacking legality. I can tell you, from experience, Pokémon has worse hack checks than most other online games. I hack Pokémon and if it looks like it was caught in the right place, it really doesn’t matter if it was hacked in or not.
Hacking in Rare candies or gold bottle caps to use on non hacked Pokémon will leave absolutely no trace of a Pokémon being hacked, infact, I transferred all my Pokémon from the Red/Blue VCV that had been trained with Rare candies it works.
(Same with gold bottle caps on USUM.)
I really think you shouldn’t care about hacking and legality checks much in Pokémon games, however I would suggest you play the most updated game of the generation.( OrAS for Gen 6, USUM for Gen 7. By playing the most recent version of your game’s it’s basically impossible to get a bad egg or harm your game save file in any way.
As for more hacked Pokémon information, you should be able to use hacked Pokémon in WiFi competitions. Anything that looks hacked will be removed from your team, hence you will be unable to use it and Nintendo will be unable to ban you. (I use hacked Pokémon all the time my entire WiFi team is hacked).
Also with the release of the switch, Nintendo is realizing it’s not really worth its time to issue bans on 3Ds games anymore.
Hope that answers(partially) the question.