If they altered your bow and didn't ask you or get some kind of blank check for service, and you aren't happy, I think they need to make it right. On the other hand, grinding the limb needn't be a problem. I don't understand from your post how the string is in contact with the limb. Purely at a structural level, a lot of mono limbs have massive amounts of glass in the limb tip area, and a responsible amount of grinding could remove quite a lot.

If this really is factory authorized service, I don't think it should affect your warrantee. Also whatever they say, if your limb breaks, but you have drilled holes in the riser for an accessory, they can't void the warrantee for that I shouldn't think. In other words the alteration would have to be in the area of the break, which of course in this case is the future concern. You could have a pro who really knows what he is dong here, and has the competence to make this kind of alteration, but the dings to the riser don't inspire confidence in me.