How do you change the way logic tells you there is a missing plug in on start up?

You can only stop those messages by removing all instances of it from the project. Then save and reopen the project, no more warnings. If you get a warning, that means it is still used somewhere in the project you're opening.

So, for your scenario there is no solution other than dismissing the warnings.

I'm on virtually the same specs, OS 11.6, LPX 3.3.

Well, I've never seen that, unless the plugin loads but needs some (often sampled) content that can't be found (which makes sense if you're on a different Mac). But normally you should get a list like that. There is no setting to enable or disable it. Can you make screenshots of two or three of those messages you get? Just use shift-cmd-4.

OK, I just disabled some plugins, but I get a cumulative report.

I actually can't recall ever getting individual messages per plugin. What version of Logic are you running on what version OS?

Now that you mention it... I seem to remember that that was the default behaviour actually, one list for all missing plugins - missing audio files on the other hand get mentioned in consecutive individual dialogs... I'll see if I can open an older project that may contain deleted plugins and see what happens...