So you’re permanent application number will be the same, just remove the X, you can check the status of your application with automated telephone service (after UCI question, it’s 1 1 2 2 (numeric part of your TFN followed by #) (your year of birth) 1 1).
As to why they assign this number is for internal process. My understanding is IRCC had to transfer data from TR to PR portal to that GCKey portal, once that is done, they are giving files a temporary application number like they would do to a paper based application. You should be able to link it as soon as the officer starts working on it, once temporary application number is assigned, I believe it’s already forwarded to an officer, so it’s just waiting in a queue.