If your roof surface has a texture to it it's most likely TPO.
"Pimples" like these are much like blisters in paint where moisture was trapped beneath the outer surface and substrate. TPO can have a polyester fleece backing to help glue it to a variety of materials. It's possible that somewhere along the line from manufacture, storage, shipping, installation, to now, moisture has gotten into the product and sunlight/heat has caused these blisters. If the roof isn't leaking I'd leave it alone.
Only cures I know of would be a) total roof replacement; b) pop each blister, inject some adhesive, roll flat, then cover with a roof coating that would stick to the TPO (which is difficult for many coatings and sealers).
Don't know how long the roof warranty is for but worth checking on. Often it's the longest warranty on RV items.
"A wise man can change his mind. A fool never will."
"You only grow old when you run out of new things to do"
2018 Flagstaff Micro Lite 25BDS
2004 Nissan Titan