I'm not an expert by any stretch, but I ran into a similar situation on my road bike. I ended up setting the FD so that I could ride the big rear/middle front combo without rubbing. If it rubs on the small cog, so be it; I just stay in the next cog or change up front.

you may be able to alter the chain line a little to improve the alignment but you may get better answers to that tn the tech forum.

swapping cassettes or chain rings around to alter the gearing may help too...