I have used Turbo tax for over a decade and it has correctly asked me about my housing allowance and related expenses. On line 7 it will print "EXCESS ALLOWANCE $xxx" if you spent less than the amount on your W-2 or 1099.
For example my Housing allowance on my w-2 might be 12,000 but I can only account for 11,000 of expenses. So line 7 of my return in T-Tax will say "EXCESS ALLOWANCE 1,000"
