1. You can edit all like window size/window bg, font in parameter plugin manager
2. Yes, the monster dex/encyclopedia is a separate system that you have to call up, so, if you don't want to use the encyclopedia, you don't need to trigger it via a script call. The encyclopedia is like the Pokédex system you get from the professor.
3. Yes, you can use items that are not for Pokemon, such as teleportation scroll etc.
4. Yes, you can change the type or name, but by default, the type currently follows the Pokémon format, so you might need to edit the “string name” section in the PKMN_Core plugin to change this. So you might need to edit a few lines of the plugin's script
Maybe you could take a look at the PKMN_Documentation.html file I’ve attached to my Itch page first. That way, you can get an idea of how the plugin works.