When my car was only 8 or so years old, and I was a much younger man, my father got me a new boot as a birthday present. This is before they were available, at least easily, as a replacement. The upholstery shop drilled my trim and put in the snaps.
It is MUCH easier to put on the cover with snaps. The snaps do take away from the original clean look both when the boot is on and off.
Years later I removed the snaps and bought an aftermarket cover. My trim still has holes in it, it's one of the things I mean to replace one day. I drive the car a lot less now so the time required to put the cover on is less of a problem. Always easier when the temps are a bit warmer. With the snap on cover I could be done in no time and on my way.
With the non-snapping after market cover I do, on occasion, have the cover slip off at the driver front outside corner. This happens when I pick up speed. With the snaps this was never an issue.
To the OP. When you remove the trim to inspect the gap, i do believe there are 'special' retainers that are used to help provide the gap for the boot.