Wow, what a crazy series of unfortunate events. At least the dealer seems to be taking care of it as good as they can.
There really isn't any mechanical engine damage that would result from an overfilled reservoir, especially with only a 1/2 quart over. It will push some out, as the dealer explained, but problems would be limited to possible contamination of sensors in the intake causing some issues with air/fuel mix. They don't tolerate excess oil very well.
I agree that the transmission issue is a separate one. I haven't seen it a lot but I have seen that leak on 6 or 7 bikes since they went to the internal oil passages and gasket between the transmission and engine. I suppose there are some casting/machining issues that occasionally occur on those mating surfaces that the gasket just can't make up for.
The limp mode issue is an odd one. Is there an actual trouble code that is telling you limp mode is or has been active? I ask because it is possible that you are unknowingly activating the idle temperature management by rotating the throttle grip forward. If this mode is activated and the engine temperature sensor has met the temperature requirement it will cause the rear cylinder temperature to shut down which lowers the idle and sounds odd. This is a total guess but I can't imagine anything oil related causing that issue.
It may also be a coincidental problem that exists somewhere in the throttle system as well. The dealer should be able to easily diagnose that issue fairly quickly with their Digital Technician computer system. They can test operate all the fuel related systems to verify they are working correctly.
I hope this helps. Thanks, P.J.