The INS alignment section and alignment procedure sections of the manual seem to be incomplete. They are missing details regarding:
The use of IFA, and what shows up in the HSI and the advisory list when GPS is active or inactive, both during alignment and when alignment is complete.
The alignment procedure doesn't mention IFA.
More clear information about alignment quality. It would be worth mentioning at least that the number has to reach 0 before alignment is OK.
The manual I've been reading from is the one linked on this page.
I was able to learn more about IFA from a YouTube video.