Hot take from a adventure storyteller: check roof-rack clearance at every entrance is not overthinking. It protects the fun part of the day. The vehicle is part of the outdoor system: it carries gear, protects backups, and must still be ready for the trip home.
Do the boring two-minute step, then enjoy the part worth remembering.
Definitely worth the extra check! Roof racks can make a vehicle taller than you think, and one low entrance can ruin the whole adventure. Better safe than sorry!