Currently when running app from the long path you need to prefix the path with \\?\ which is causing that AppDomain.CurrentDomain.BaseDirectory also starts with that. Some apps might pass the directory into component which doesn't expect it (in .NET Framework BaseDirectory could be an URI so some apps could have passed it into Uri which would throw if it encounters anything starting with \\?\).
See #58627 (comment) and #58712 for more context