How do multi abilities change team building in Elite Redux?

Bit of both. Every mon has its normal ability plus innates that are always on, so think of it as stacking. A mon with two innates that work together can be far stronger than its stats suggest, and that's why early fights feel unfair. For your own team that flips the usual order: pick mons for their innates first, moves second. Read the innates on the summary screen before you commit to anything. For trainers, I look up the gym leaders and rival fights since those are the walls, and just play the route trainers blind. Losing a route trainer costs you nothing.