I don't recogn' I've ever had multiple plug in windows active simultaneously while minimized. It's quite difficult to locate minimized windows (imo) when working.
Are you familiar with the "Recycle Plug In" option in the Preference>VST setting? This will use the same recurring plug in window if you only need to work with one plug in at a time, meaning it allows for only one instance of a plug ins window to be opened, but will change out for whichever plug in you chose to work with. It's pretty great for quickly moving through plug ins without the need for minimizing or exiting out.
So, in most cases working through plug in interfaces, I use multiple opened plugin windows only to compare settings when utilizing a dual mono/stereo process method (I probably made it up and is a waste of time?...) using channel strip emulators but gladly rid of them once set..... I love the feeling of moving on to the next situation!
Needing access to the plugin interface is instant when launching it by clicking the plug in, wherever it is inserted. This method should also improve performance unless you are on an older machine using new 3rd party plug ins that take time to reveal themselves (I have an older laptop for useless conveniences that takes 30-45 secs to load the Waves SC Omni Channel...I should probably use your method of just minimizing its window lol)
....I'm a bit verbose, yet I do not know why.