Yeah, I also agree with Chuck. A lot of it depends on who makes the ARF. Sig or Hangar 9 I will use the supplied hardware. Some of the older Hobby People/Shack stuff I would replace most of it.
I always round file the engine mount screws and use socket head standard sized screws.
Had to replace all the the cowl and engine nacel cover screws on my new Twinstar as they screwed up (no pun intended) and supplied machine screws.