Hi Tom,
I can appreciate your feelings regarding keeping things out from under the glass, over and under cuts on the mats etc. Sometimes, you just have to learn to leave things as they are. The more you fool with things the greater the likelihood of damaging the photo, glass, and mats if you keep trying to remove dust, etc. Unfortunately slight over and under cuts can not be avoided. We try to as much as possible. But, this comes about in many/most instances because the boards (frequently as they arrive from the mill) are not totally square. As a photographer, artist, frame shop, etc. we try to minimize the problem and correct them to be the least noticeable as possible. My friend who is a custom framer tells me that the rule of thumb is you get things as perfect as you can so that it is not visible at arms length.
Rich