so does this mean that any RTA tests i might attempt might be slightly skewed because of these pops and skips?

Only if you're doing sweeps as opposed to full spectrum bursts, and only if you're depending on a "single pass" for the test (you shouldn't anyway).

When I do RTA, I have it looping a track constantly with continuous monitoring and updating. And by the way, I've never heard any of my short RTA test tracks skip. I don't usually keep long songs on the player for day to day listening, but I would imagine that if there were dropout problems they would probably only happen on long songs.