Major INDI Library release v1.9.0 bring significant internal changes championed by @pawel-soja to modernize core INDI Library drivers and clients. New drivers for DeepSkyDad Flat Panel & Pegasus devices plus further improvements to PCM8 drivers.
No, not all pop ups. Only the applications that you would switch back and forth. A notification like covering the scope should be left as is. You typically just see those and close them. There would be no need to keep them active in a tab.
Because I have two screens I prefer the concept of multiple windows.
There is only one annoyance: EKOS is minimized together with KStars' skymap window. In don't like this behaviour. EKOS should stay open if I try to minimize the skymap window.
I'm running Kstars 3,5.1 with Catalina 10.15.7 and cannot replicate this window behaviour. "Independent Window" for Ekos/Indi viewers ON or OFF seemed to make no difference. In full screen mode Kstars filles the screen as expected. If Ekos is opened I get a floating window and once Indi is started it's in front of the Ekos window. Clicking the Ekos window doesn't cause it to move to front. I have to hide Indi (from KS tool bar) to see Ekos again,