You should not need to create the homekit.cfg file, at least I never have on OH2. I’m not sure why the documentation says that since everything in the file is a duplicate of what you configure through the Paper UI.
That said, I’ve found Homekit to be a fickle beast. It has always been a fight for me to get it to pair successfully. You might take a look at this thread. Specifically the part about clearing pairings and allow unauthenticated. I wouldn’t think that you would need to clear the pairings given a first time installation, but maybe the failed attempts fowl something up.