It can run without Play services (it does for me). I'm sure the code is there somewhere in the APK, but since it doesn't actually execute if you're not using Play services, I don't see a problem with that.

They've also not categorically dismissed F-Droid; just given a list of things they need it to do first. Some of those have been resolved by now, some are unlikely to be any time soon.

You are unhappy and disagree with the decision but are they really "red flags"? In the GitHub issues you mention Signal does provide what seems to me to be good-faith reasoning behind their decisions.

Yes, I definitely see those as red flags. And I'm not unhappy, just being helpful for those who maybe aren't paying close attention. Would hate for them to end up in another WhatsApp situation!