FMCB can boot from either slot. But for some reason, many PS2 games only ever read from Slot 1: they don't even give you an option to use Slot 2. I don't know if there are technical reasons for this, or if it just became common practice for some reason.
That's the core issue here. It's not really about putting your FMCB card in Slot 2; it's really about putting your game-saving memcard in Slot 1. FMCB doesn't care where you boot from, but many games do care where you save to.