Is there a way to enter the "net" medical expenses after HSA payments rather than entering the gross medical expenses and letting the software deduct the HSA money?

The amount of HSA distributions will carry automatically to Schedule A, and there is no way around this.

However, it is sufficient to add a single medical expense line with the description "HSA medical expenses" and the amount equal to the HSA distributions as an other medical expense (you can do this at the end of the Medical interview).

This will offset the HSA "reimbursement" and keep Schedule A in balance.