@Imperium As you can see, I opened an extra thread for your second issue (the “Always on top” setting).
I moved our discussion now into this new thread, as the our posts turned out to be mainly about the loss of the “Always on top” setting now - and as your first issue (“Start to tray” not working) was already dealt with in Current bug: Desktop app doesn't "start to tray"/minimized (though set as such) (and fixes for that are already on it’s way).