I have a couple glass carboys and a better bottle carboy. I actually do the opposite: primary in the better bottle, and move to the glass for secondary. While it should be fine, I prefer to use the glass anytime I need to secondary, which I tend to do for longer period.
Also, if you want to play with sours like I do, the better bottle is probably not the best choice for sours. Don't want it to pick up the "infection" from the sours and pass it along, which is easier if you don't take good care of it (can be rougher with glass).
But Revvy is right, no reason you can't use them. I like mine.