I have tried using KStars/Ekos on both an x86 MacBook Pro as well as an M1 MacBook Pro - and I see the same results on both with regards to the hidden dialog / modal windows. The dialog window issue does not appear to be related to Mac hardware for me. The only way I was able to figure out that there was a hidden dialog window open was that I was taking notes on the crashing issues and just happened to move the Ekos and Kstars window out of the way to jot down some notes in a text editor when I happened to see the little Port Chooser dialog open behind all other windows. Otherwise, I would have never figured out what was going on.
I have not had any crashes since - but I have not yet used everything for an imaging session - only testing on the bench. So far this is working for me:
Sky-Watcher AZ-EQ6 mount with EQMOD cable
ASI 1600MM-C main camera
ASI-120MM-S connected to 50mm Guide Scope
Moonlite Focuser / Stepper Motor with Moonlite controller
My INDI server (miniPC / Quieter3Q) is currently connected via ethernet as I am not ready to start worrying about WIFI issues yet.
INDIWebServer - whatever the latest is