To clarify about the video thing, I don't know which video you're referring to. This question came solely from my own curiosity and the fact that I want to remain as safe as possible when it comes to creating Pokemon through PKHeX.
Also, I haven't even once gone online with ANY of my Pokemon that I have made through PKHeX, and I will not do so until I am certain I am able to make a Pokemon that is "100% undetectable (in terms of legality/legitimacy). Furthermore, I had already planned to make sure that once I do first introduce a hacked Pokemon, I've looked through it thoroughly (almost obsessively) to make sure that not only is it "legal", but raises absolutely no red flags, and once I DO introduce it, I will not make any further edits to that Pokemon, because I had thought the same thing you're saying (About introducing a Pokemon and then editing it and reintroducing it)
However, I am novice to intermediate (more on the novice side) on what raises red flags. So, my main question was this:
Of the things I've listed (And anything else you can change, but mainly the ones I've listed), would any of these changes end up raising a red flag because it does not correlate with the correct SID, TID, PID, Encryption Constant, etc? Or are all of those examples completely independent of other changes themselves?
Just to clarify, let's say I change a Mewtwo I caught from Naive to Timid. Let's say I change the Poke Ball, or any of the things that I listed. Do any of these value swaps affect anything besides the immediate swap itself? As in, by editing <whatever is on that list, may it be 1 or more things>, does anything else *need* to be changed in addition to that, in order for the Pokemon to remain legal and not raise any red flags?