Yes, I used to have a meolodeon that had B major, which meant it sounded wrong for some tunes. The one I have now has a stop for taking the thirds out of the chords, which leaves a nicely vague open 5th.

I think it's quite important to understand that the G-C sequence is not paralleled on the D row basses. If you try using the B buttons where you'd use a C, it ofen sounds weird. You can, as Anahata says, forget about this until later, but this means you have to un-learn a way of doing things, and it may be easier to learn to cross rows from the start. The equivalent sequence to G-C is D-G, which you can only get by crossing to the other row of bass buttons. This means you have to play certain melody notes on the push rather than the pull, so you may have to cross rows for this as well.

It sounds a bit tiresome, but the earlier you learn it, the easier it'll be and the sooner you get used to it. Otherwise you'll always have this uneasy sound of not-quite-right chords when you play certain tunes in D. Some melodeon players try to avoid playing in D at all because they can't quite get their heads and fingers around this, but that's a bit of a waste of a two-row instrument.

Marje