Hello... from time to time in my build's, there will be a motherboard hole that will not have a case mount... you will be fine, if that hole is not grounded to the case... the problem that can occur, if you try extreme pressure, inserting parts, at that location, cracking, bending the motherboard, so becareful.
some cases have pre installed standoffs some can be moved some cant. most time the good mb vendor use one standoff to line up the mb. most times it the top center standoff or the mb center standoff. all you want to make sure is that the mb does not touch the mb tray and short out.