Long time reader, first time poster.  On a sale, there is no need to over-estimate the transfer taxes and stamps nor collect for any "possible rejection." It is pretty simple to calculate it right.  Also what lender or realtor client would allow such excess charge.  The lender should make the title company remove it before closing.  If I was the seller and it was collected from me, I would force their hand by not agreeing to the HUD-1.

Problem does arise on refinance transactions where parties want to remove parties and/or add parties to title.  As you give your estimate the consideration is constantly changing as they make payments.  This is especially true as refinance approvals are taking any where from 30 days to 6 months in many of my cases and most of these transactions require transfer taxes to be paid on the transfer and recordation taxes on the transfer and the new mortgage/deed of trust.   When the new GFE and GFE rules were created, this was my only problem with it. Still a good title agent should be within say $100 or less, disclosed on the GFE, and refunded back to the borrower's if any excess remains.