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Those settings will be saved (if they’re not i will fix it) in a per-project basis. Once you set them in the project they should stay like that with every project load.
Setting any of those options as default when loading the VST plugin in the project for the first time is a bad idea, passing unwanted MIDI can cause loops or hangs in some configurations so it must be left to the user to set them per-project, those options can change in every project depending on what hardware you are using and how you are routing MIDI.