It seems to be working correctly for me.

If I have the Home Office as 10% of the home and enter $10,000 on Line 10 of 8829, it properly deducts $1000 on the 8829 and puts $9000 on Schedule A.

In the event you don't want it to flow to Schedule A at all (you want to manually prorate and enter the amount on Schedule A), there is a check-box on the "Smart Worksheet" right above Line 10 of the 8829.