@LarsGit223 oops I thought you had taken over this one, sorry and apologies to @techee :-D
My reasoning for why plugins should use the settings from Geany (assuming they have the same basic form) is that the Geany settings exist even if the plugin is not loaded, and they don't go away if a plugin adds another version of the same setting. So now there are two places for the same setting. And one is used in some places and the other setting is used in other places. That leads to the sort of confusion the OP reported.
Obviously if the settings do something different and there is a good reason to have both then fine, just clearly document which functions use which setting, and possibly why, so users understand the thinking behind the decision.