I have several questions I hope are simple and not off topic.
Is there any functional observable difference between a normal pokemon and a pokemon made by PKSM that abides by available moves? Is there any harm to wonder trading fabricated pokemon? I know I've gotten a few shiny mythics that couldn't be naturally occurring.
Does raising a pokemon's level with hacks do anything to make it weaker, assuming EVs are given? I ask because some of mine have seemed feeble, though they might have just been feeble pokemon.
Are legendaries given a set number of IVs everytime or else given a set value to their IVs? Or are they at all random. I ask because I'm prone to moving IVs around with PKSM and don't want to make anything illegal.
I was most disappointed recently when I captured a Mewtwo in Ultra Sun and the game wouldn't let me name it 'BiggSexxxy' after professional wrestler Kevin Nash as I had back in my Gen 1&2 days. Will it create any problems if I use PKSM to override its nickname?
Is there a simple way to activate the national pokedex with PKSM? Otherwise is activating it as easy as downloading Pokemon Bank via Freeshop and not subscribing to it?
To answer your questions:
1. Pokemon that are edited or genned cannot be identified as such so long as it is within possible parameters. It is impossible to notice any difference in game and, to my knowledge, not visible from a coding perspective either. No harm in Wonder Trading, but do know that some people who dislike hacking frown upon receiving potentially hacked pokemon.
2. Raising a Pokemon's level through an editor does not make it any weaker than normal, but it would miss out on receiving EV's from defeating other Pokemon. Since you are tweaking EV's anyway, then that problem is fixed.
3. Some legendaries do have IV restrictions. You may want to double check this on Serebii, but to my knowledge legendaries had completely random IV's before gen 6. Starting with gen 6 and onwards, pokemon in the No Egg group have a minimum of 3 perfect IV's, but which IV's are perfect are random. The remaining IV's are completely random.
4. In regard to the name filter, I don't know what will happen. I imagine that it would be fine until you bring it online, and at that point you would be told that the pokemon was inelligible.
5. For the national dex, it is actually a feature of Pokebank, and can only be viewed in the Pokebank app. Nothing this can do about that. Requires a subscription too, which is a bit of a shame.