Here you can find some tutorials. Ignore the compiling tutorial, you don't need that.
https://projectpokemon.org/home/tutorials/save-editing/using-pkhex/
I don't know what you are talking about. But if you want to clear/apply trash bytes just use PKHeX for that.
Ctrl + Click on the Nickname/OT field, then you can clear/apply and modify the trash bytes.
Mankey and Bulbasaur do not exist in Legends Arceus, so you can not convert them. Same with Onix which does not exist in Scarlet.
Mankey exists in Brilliant Diamond, so that one works.
Starting with Gen 8 GameFreak decided to cut some Pokemon out of the games. They don't even have data/models for those. Some Pokemon might get added through DLCs while others will remain unavailable.
Well, it's exactly like that. There's only PID, Moves, Species, HeldItem, Level and EVs (not per stat, only one value that's applied to each stat).
PKHeX already has the data structure, it's just missing a GUI.