I think I have experienced the same "bubbles" that you are referring to.  I owned an American Tradition motor coach  that had the same thing mostly on the the edges of the roof.  An inquiry to the manufacturer resulted in the following explanation.

The rubber material is applied to a wood substrate and every effort is made to ensure that no air bubbles exist, however, wood is a porous medium and the possibility exists for air to get trapped between the substrate and the rubber membrane.  These bubbles are harmless even though they may increase of decrease slightly in size with varying air pressure.  An increase in the size of the bubbles may appear larger than normal in the event the unit is taken to elevations higher than normal.

Personally I thought it was just a bunch of male bovine defecation from the company but I owned the vehicle for just over 5 years and after taking it into the mountains several times the bubbles did get bigger and shrunk when I came back down just like they said they would.  Other than irritating me, they never caused any issues with the coach.

My fifth was manufactured in 1994, It's been exposed to the Southern California sun 7 days a week since we bought it, it has travelled from sea level to 8000 ft numerous times over the years, there have never been any bubbles between the substrate and the rubber roof membrane. The bubbles would indicated a poor glue job by the factory. I would expect the bubbles to get worse over time as the membrane flaps in the breeze and pulls at the glue.

I wouldn't consider them harmless....I'd want them fixed before warranty ran out just in case they got worse.

For example, the other day I saw a fifth wheel trailer being towed on the otherside of the freeway. I saw a dome shape on the roof at the front of the fifth wheel. At first I thought it was some new type of In Motion Satellite dish dome. As the fifth wheel got closer I could see that it was the roof membrane bubbling up. The bubble was bigger than the satellite domes you see on RV's. It appeared the membrane was still attached at the front of the fifth wheel and down the side I could see. So this seemed to be caused by the vacuum created by the air passing over the top of the trailer. Which would mean all of the glue had let loose in the center portion of the roof. It was a smooth side fifth wheel which means it was probably built after 2000.