It's not the best thing about reaper for sure.
I get around that with one larger monitor and docking the mixer to the left.
You can then drag the track panels of the arrange screen out of view giving you a small skinny arrange to the right. Even open a master track window over the top of it.
Toggling the mixer visable or not with a key command will give you that and the arrange windows view as options with plug ins not hiding.
They only go into "bug view" behind an undocked mixer window - a pain for double monitor folks.
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