Opening a UFO, making changes, then exporting as UFO now causes custom keys to be placed inside a dict within a com.schriftgestaltung.font.userData key. That shouldn't happen. Custom keys are just that - and shouldn't be altered by Glyphs. That's not your data, so you shouldn't be messing with it. Other tools depend on these keys, and you've broken them!
I've also noticed that you are now storing within that key some of your own fields. That is also unnecessary, though you are welcome to do that. The problem is that you continue to export the same keys outside your new dict, so that a number of your keys get duplicated. This bloats the lib.plist (especially with thousands of items in .glyphOrder!) and it's not clear which version of the keys is authoritative or maintained.
Please be consistent in where place your keys, delete your keys from places that are no longer current, and stop moving other people's keys around!