Line 14d? You mean line 14b?
The workaround to round numbers on the 1099-SA is OK. The IRS gives tax software vendors the right to round numbers as they come into the system, so when you round those numbers, you are just doing what TurboTax is doing.
From your description, the issue seems to be that while the distribution amount is probably rounded when it comes into TurboTax, the amount of qualified medical expenses seems to be handled differently.
I assume that the 1099-SAs are copied to the IRS (they are supposed to be); however, for the reason in the first paragraph, I have trouble believing that this will be a problem.
There is no harm in fudging in TurboTax in order to get the correct output on your tax return. The non-zero number in line 16 is certainly incorrect, as you say, so you are permitted to do what you need to do in a software product to get the correct output.
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