RapidWeaver shouldn’t be loading the plugins based on what project you opened or didn’t open.
The “Could not obtain Plugin Principle Class” is the message that you get when RapidWeaver tries to load a plugin at startup from the addons folder.
If you need any plugins that aren’t yet ready for the new Apple M1 chips then you need to run RapidWeaver under Rosetta.
If you are sure you don’t use PlusKit then you’ll need to physically delete the plugin from your addons folder.
If you don’t believe this close all projects, close RapidWeaver, and reopen RapidWeaver without any project open. You’ll still get the message.
As for when PlusKit will be ready for the new M1 chip (universal build) is a question that’s been asked multiple times without any answers from @isaiah .