My point is this: consider you have an NMO mount and drive/park somewhere there's a low branch you don't see. The collision with the NMO will not be near as nice as merely "tipping over" the mag mount.
Not so.
I had a Larsen wide band 1/4 wave whip on a permanent mount. These are thick/stiff whips with a spring at the base. This was on top of my personal 4x4 F-350 with the aluminum body.
I knew it was up there, but pulled into a parking garage in Las Vegas last year (or maybe the year before…) It went from plenty of room, to narrow ramp with a low overhead and a line of traffic behind me. There was about 3" of clearance between the roof of the truck and the overhead stuff.
The spring on the base of the antenna took a permanent bend to the stern, but there was -zero- damage to the NMO mount or the aluminum roof of the truck.
I went online, ordered a new spring and was good to go. In reality, it really didn't do much to the antenna, but I wanted to replace the spring just so it looked right.
I've got an F350 4x4 service truck at work with two permanent mounts on it. Aluminum body also. WB 1/4 wave VHF whip and a co-linear 800MHz antenna. I've taken that truck up lots of access roads with low branches. I've got permanent green stains on the headache rack from tree branches. I've had to run through two tracks that haven't seen a vehicle in years, very overgrown. I've bent the headache rack on a branch. No damage to the permanent NMO mounts or antennas.
So, no, a properly installed NMO permanent mount will not damage the roof in a low clearance situation. Use the thin 1/4 wave or 5/8 whips and they just happily bend over and go on with their day, no issues. The thicker antennas with the springs will take all but serious hits.
On the other side, I had a friend who loved mag mounts and used them on top of his truck for the exact reason you do. He hit a low branch, knocked the mag mount off, and left a big scratch on the side of his truck and dragged the mag mount along the street before he stopped.
If you want to use mag mounts, go ahead, I don't have any problem if that is what someone wants to use. But they are not a superior solution by any means. As more and more vehicles go to something other than steel in the body, mag mounts are not going to be much of an option for newer vehicles. I do have mag mounts, but I use them for testing, or tossing on top of a file cabinet for indoor use.