I'm really happy that Paizo decided to go with keeping them large. To me one of the main draws of playing a Centaur or Minotaur is that those are a freakin half horse half human with all that comes with it, or big horned bovine humanoid. The size to me was part of the fantasy. The D&D way is just reflavored humans not a new ancestry.

As for balancing, there is the whole "what if another PCs rides the centaur" scenario (which you still have with pony centaurs and small PCs) and the reach and using larger weapons for more damage dice issue. I think the first isn't an issue at all in PF2e and the second, well, I am curious.

Going about reach and big weapons by just saying "but you don't have this" would seem weird. Those are generally applicable rules in the game system. But offsetting them with downsides would be tricky as you'd need a lot to make up for those upsides. Then there is grappling larger enemies and immunity to small grapplers but also the whole "I don't fit through this" issue which is a downside but can halt adventures completely. I hope Paizo find a good solution, I don't have one.