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They absolutely do overwrite, that's what allows plugins to even work in the first place. Most plugins would be pretty pointless otherwise.
The issue is that def pbInitPokemon needs to exist in the base Essentials files, because the Shadow Pokemon script depends on it existing so that it may...
I'm assuming the only reason you're using :ELITEFOUR_Agatha instead of a battler index is because you want to use a different sprite from the the trainer sprite? If that's not the case, you should just use an index, it's much simpler.
Anyway, this just seems like there's a bug when using ID's...
The mechanics for these forms work completely differently. Zacian's item doesn't change its form, Zacian just naturally always tries to change form when it enters battle, it just fails to do so if the required item isn't held.
Ogerpon changes form outside of battle, upon equipping its held...
Only one variable is coded into the script. However, you can always just use the regular $game_variables in a hardcoded script if you wanna do something more elaborate.
Minor Update (v1.1.3)
Fixed a crash that could occur when setting custom music for a battle through a battle rule.
Fixed an issue with low HP music ending when Pokemon with critical HP is on the field, but a healthy partner Pokemon is sent out, or a partner Pokemon is healed out of the critical...
Major Update (v2.0)
This plugin has overgone extensive changes that brand new functionality as well as updated graphics and overhauled code.
UI Polish
The entire UI has been given an additional coat of polish. Opening/closing menus or jumping through pages with the JUMPUP/JUMPDOWN keys now...
You have to set the form in the trainer PBS file. Idk if its a bug or not, but Essentials doesnt automatically set the appropriate form for trainer's Pokemon that hold items.
"setVariable" will never trigger the "Variable" keys. Only "addVariable" or "multVariable" will. This is mentioned in the guide.
"setVariable" is designed as a reset option to return the variable back to some base value. Its not designed as a means of triggering any keys.