This is probably a simple answer, but if a ship with Swarm Tactics uses it on a low PS ship (e.g. Academy Tie) then a ship with Predator would not be able to roll 2 dice against the swarmed Academy Tie, right?

Example:

Howlrunner swarms an Academy Pilot to PS8

Ship with Predator attacks Academy Pilot but can only re-roll 1 dice due to new pilot skill during Combat phase.

I had a couple games the other day against a roark squad where i had predator, and I used 2 rerolls against ps2 ships that had gotten ps12 from roark. Never even occurred to me or my opponent at the time that I possibly couldn't.

I think you are probably right though that you couldn't use the 2 re-rolls for predator.

...treat the chosen ship as if its pilot skill were equal to your pilot skill.

No limit or condition there on only treating it as equal for a given purpose. Bring them up via Swarm Tactics, Predator doesn't get the bonus.

Similarly, a pilot who had his PS reduced due to a Damaged Cockpit (I think that's the one) would eat the 2 dice reroll.