What qualifies as a "fitness breakthrough?"

Is it just that your actual output exceeds your MPA? Does obtaining a “fitness breakthrough” cause an adjustment of other fitness factors?

That is correct, although it you generally need at least 5 seconds at or near MPA for the breakthrough to count. When this happens, your fitness signature will change.

Today’s ride showed a bronze “trophy” symbol on the Xert field on the Garmin 520 but the uploaded ride does not show as a “breakthrough”. Why not?

Similar question for me here, I’ve just completed a session and Xert automatically updated my fitness signatures, but hasn’t flagged it as a “Breakthrough”.

I’m guessing this may be because I didn’t spend long enough near MPA, but by exerting a Peak Power higher than the old value, the signatures clearly required a change?

Yup.