Using screws longer than 8mm with a 5mm thick mount will result in damaging the T- slots.
Using a mount thinner than 5mm with the supplied 8mm screws result in damaging the T-slots.
If you are wanting to counter bore the screws make sure the distance from the back of the mount and the counter bore shoulder is 5mm when using the supplied M3 x 8mm screws.
Using screws that are too short won't damage anything, it just won't be able to fasten the screw into the square nut.