Hi,
The XT rear derailleur will work just perfectly with you combination. I run a similar system just with different shifters and crank and it works a treat. I cant see why a crank form a different manufacturer would change the rear derailleurs performance. If an ultegra derailleur will work then an XT will work also. Last year I put an XT long cage derailleur into my compact road bike and it worked a treat.
As for compatibility, all Shimano Dyna-shift 10 speed derailleurs must use Shimano Dyna-shift 10 speed shifters. This may be the source of the confusion for your bike shop mechanic. 9 speed xt derailleur will not cause a problem as they are compatible with your system.
I wouldn't really consider anything else, I saying that the Deore one would probably work very well too.
Good luck with the build,
Donnie