90-100 days is not uncommon as most incubators do fluctuate 2-6 degrees, which is fine... Typically last year I saw 86 days at 82-83 degrees on average, if the incubator remained at an average of 86-87 then the hatch time was reduced closer to 65-75 days...
As for your vet, I would find a new one if they are tell you your dragons can die due to suffocation in the egg. The egg's membrane is very thin especially close to hatching, and gas transmission of both Carbon dioxide and oxygen is very good. If this was not true your embryos would never develop and remember in the wild they are some times buried up to 3 feet deep in clay!
Seriously finding a good herp vet is very hard these days, as a lot don't specialize or spend enough time around bearded dragons to know what they are talking about... Chances are their experience is coming from a text book that's 20 years old or they are basising that information off another lizard, in either case you can't just infer from another species..., Captive breeding is an ever evolving trade, and what's right for iguanas, or geckos is not the same for bearded dragons. New and healthier ways to executing certain techniques are discovered and shared everyday between breeders and hobbiests, so unless you are submersed in the culture/community and deal with dragons on a daily basis you fall behind very quickly! Ask around to see if anyone in your area can recommend another vet, even if you have to drive a good ways it's worth it to have an experience herp vet that is up to date on current information. I really can't believe your vet told you that... :?
Anthony