Would having 2 years of non-rated time for the CA Qualification Course and SOCM hurt you for promotion?

You get an AER for that. The 1059 is rated time. As long as they have an eval that goes up to the report date and another that picks up after the graduation date, there is no unrated time.

Not really, 2 years for 18D or CA plus SOCM is the only way to get to that job, and everyone there (the peers you compete with for SFC) all look the same after that path.

Your school time is not non-rated, you should have come out with a DA1059 that will cover you for that period.