I perused a French-language bike touring site and one tandem owner said that you can usually get a tandem on TER trains, but that the newer cars are much better than the older ones. For Corail trains, he recommended to get on the last car in the train. He said there's usually space there and being the last car, you won't be blocking anyone. I would suggest that you do not ask permission. Rather, just get on the train with your bike.
I took quite a few trains in France last year with my (non-tandem) bike. The TER & Corail trains all seem to have space and hardware set up for passengers to mount their own bikes. It couldn't have been easier. I was on a couple of trains with very few passengers, and the ticket takers were very relaxed. Once, I didn't even bother taking off my panniers and I just leaned my bike against the side rather than hanging it on the hook. The ticket-taker didn't mind at all.