Personally, I am skeptical about going thru the hassle of having an entire new roof installed when minor bubbling could be fixed by another, simple means.
Our CY has had a few small bubbles on top, but haven't gotten any worse thru the years yet. This is a non-issue now, but if I ever get the whim to repair, I have my own repair method.
Quality water based exterior glue, wax paper, weights, tape, paper towels, bucket with water, and my poultry injector with the 3" needle.
Inject SMALL amounts of glue thru rubber in as many places as needed for each bubble. Press down the rubber to squeeze/spread glue around, cover all injected perforations with wax paper, tape paper down, and weight down that entire bubble for 2 days. The worst thing cosmetically that may need to be done is a dab of Dicor on each needle mark, but I doubt it would be necessary if glue oozes onto the wax paper.
Your bubbles on the rolled sides could also be done same way, except without weights. After smooshing the glue around, use long strips of tape from good part of roof, around wax-papered edge, and onto trailer siding to apply the smack-down theory.
I used this same format to fix our CY's delaminated plywood slide bottoms. On the bedroom front side of slide, I let the sun warm up my glue...BIG mistake! The other 3 repairs, the glue went into the refrigerator beforehand....MUCH better!!