So the all users controlling the menu thing isn't the actual problem but the real problem is being worked on anyway? I'm confused about what controller issues were fixed, since changing Port 1 to the Pro Controller still softlocks the console.
"All users control menu" being gone is not a bug or issue beyond being inconvenient. The feature was simply removed and hasn't been replaced yet.
For a long time, disconnecting then reconnecting a Pro Controller or Classic Controller literally did not work, the controllers would not function at all, as player one, player two, or any higher numbers you might imagine. This wasn't a menu issue, it was RetroArch-wide. This issue was fixed.
The second issue, the one you're talking about, is that manually changing the controller order is broken. This issue is the one I said quarky is aware of but is not fixed yet.
For what it's worth, changing ports automatically is working correctly, so if you want to use a Pro or Classic Controller as your player/port 1 controller, you can just move the Wii U GamePad away from the console to stop it being mapped as port 1. RetroArch will just map whatever controller is available first to port 1. If the GamePad is around, it will always be available first.