Most of what I had to cut around on the carpet were pretty easy, so it wasn't a big deal to do the carpet last. One of my concerns was also that if the carpet goes up first, there may be a small amount of movement between studs and the ceiling panels when you start to build walls because you are going to have the spongey carpet between the stud and the ceiling. The carpet may add a little "give" to the walls/studs when you fasten them to the ceiling.
As for the odors, that has not been a problem for me. I have the traditional vent fan over the oven and and additional fan up on the roof behind the drivers seat. The carpet is not going to absorb any more odor than the couch, chairs, ect will, in my opinion. No one has ever came in the bus and told me what I had for dinner the last night and my carpet has been up now for well over a year. I think it really depends on what you think looks good in your bus and what works best for your conversion.