A small round file sould do a pretty good job of it. A dremel may be a little harder to control if you're not used to it.
It's a real mystery to me why these manufacturers are having this problem though. The specs for 5.25" bays are well documented and have been around since the dawn of PC's. The weird thing is I've seen Lamptron controllers that are right, so it would appear that they are outsourcing the chassis work (pretty common) and one or more suppliers have the wrong dimension. You would think it would be picked up by Lamptron's QC department
It's a bigger problem today, because so many "tool-less" mounting systems rely on locating pins to lock in the device.
I really don't want to change the current mount, since it makes it very easy to install a correctly designed device, but I agree, it's a problem needing a solution. I'll look at coming up with a mount that allows some adjustment. I should be able to get that done pretty quickly.