No, it's OK.
Yes, the Self box will be checked, but Line 3 will have zero or none, showing no coverage, which is what you want.
If the IRS ever writes you a letter about this (I have not heard of them doing this), just explain that you were dealing with a workaround in the tax software that you use. Since all your numbers are correct, that should not be a problem.
How do you plan to deal with the carryover? You have two choices:
1. Apply it as a "personal" contribution the next year in which you have HDHP coverage, or
2. Make a distribution equal to the excess, but when the 1099-SA comes, enter it in TurboTax saying that none of it was for qualified medical expenses. This will add the distribution to your Other Income as well as add a 20% penalty, but the excess will disappear.
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