I'd say the dark spots are blister divots that have been repaired with a filler. Interlux Watertite sets up pea green/purple. If the stuff is all solid and dry, my experience is...leave it alone. If the boat was in the water for a season, and you cannot see any evidence of active blistering, roll on a few coats of Interprotect just as a base for fairing, paint and go.
Certified...in several regards...