It's not hard to do, but you do have to fab up a spacer to make up for the lack of the thickness from the thermal pad. Here is a pic showing what I mean:
Yes, things could go wrong. You could damage a FET or something accidentally. If using the wrong thermal compound and it squishes out onto the FET leads, you could cause problems. There are always risks to modding. You just have to weight the gains vs the risk. I thought it was worth it, but then again, I'm comfortable with this type of thing.
A couple people here have sent in a modded Quark and they honored it, but one person also got a note back with the repaired ESC saying that they wouldn't honor his warranty again. So, I dunno. I would err on the side of caution and assume they won't honor it.
What you could do is run it as-is for now and see how it goes. At least add a heatsink to the outside of the case (that won't void the warranty). If temps become a problem, then you can decide if you want to take the risk in modding it.