I couldn't believe the discrepancy!

If I understand your response, you are saying the best way to ensure the LLC is fully realized and prevent a discrepancy (Mortgage in my name and title in LLC's name, is to refinance.

The standard printed exception as to discrepancies, conflicts, shortages in area orboundary lines, encroachments or protrusions, or overlapping improvements:(i) will not be amended or deleted from the title policy; or(ii) will be amended to read, "shortages in area" at the expense of Buyer Seller.Why would I choose (i)? 

Typically there's a pretty big discrepancy, but it's typically one that goes in the opposite direction (tax assessed is way under market value).

Although that does sound like a big discrepancy.

We had a fire and ended up with a huge discrepancy on a 4 plex.

Before closing on the property, get their lease and have an Estoppel Agreement signed by tenants to see if there's any discrepancies with their lease.

Where the discrepancy comes is if that owner “blocked” off days intentionally, or if it’s truly rented.For example: I have an Airbnb at the Jersey Shore.

Look for discrepancies between the trailing 12-month financial statement (T12) and their year 1 pro forma.

And have some cash reserves for repairs you may have to do on the property and any other discrepancy that will occur.