bondo / isopon p38 is a great filler . it sets rock hard in under 10mins if mixed correctly and can be worked on in just over 15mins.
any other filler used for wood , including the plastic based types ( rawlplug plastic wood filler for example ) take ages to set and
sometimes in the sanding stage , chunks can come away leaving the user to re-apply more to cover the flaw.
the only downside to using bondo / p38 on bare mdf , is that the filler is harder than the wood ( its polyester )
and the mdf sands easier than the filler . this can be a problem when trying to get a proper smooth finish as
the area around the hole can be sanded away more than the filler itself . bondo is designed for wetsanding and you
need to be used to handling it / sanding it / working with it to get the best from it , especially if you are not using water.
and lastly , while i do reccomend the use of bondo / p38 as the best filler out there , dont use a water based
filler on mdf , for obvious reasons . but any filler out there should work okay for you . just watch out for the slow curing type
as you cant fill a hole in 1 go with them. you have to apply it bit by bit and then sand it back.