Secure Flight is crap...don't pay it any attention...and you don't need to do the 'registration' with your airline unless they force it to complete the registration.

There is no checking of your secure flight inputs against your PNR at the checkpoint - just make sure your boarding pass name matches your ID name, although the absence or inclusion of a middle name on one or the other is not an issue. The screener has absolutely no way of knowing what information you gave SF - for all they know, you could have named yourself 'Baba Ganouch' on their system.

My DL has my middle name...my BP does not. No issues. I have not 'registered' for SF with my airline. No issues.