would it be possible to make the compacting drawer compatible with the fuel pellets from Progressive Automation? or does the mod autodetect the 'nugget' recipe?

It autodetects everything that can compact and uncompact again (as a 2x2 or 3x3 recipe). If it doesn't work, you can create your own rule with the MineTweaker API.

It probably doesn't autodetect because you get 8 fuel pellets instead of 9. Also, there's no reverse recipe, because fuel pellets can be made from either coal or charcoal.