I've had a few tents and had similar clearance issues. Yes you can store the tent sans ladder.
Two of those tents we're taller than the height limit, so everytime I installed them - which would be a few days before a trip, afterwards I remove it again- I would do so without the ladder. On one of them I removed the ladder completely, the other I simply removed the lower section (which slides right off)
On the one I have right now, the ladder is stored in two sections, one to the side of the other instead of on top of the other. This gives me about 1.5in of clearance so I can safely enter the garage without hitting the ceiling. It is tight, if I brake when passing the entrance I can hit the ceiling, but I can get through no problem.
If budget is not an issue, I believe hard shell tents are of a much lower profile than folding tents, which are the only ones I've used so far..