This is NOT tax advice, but... I ran into exactly the same problem. Customer support has nothing on file about this issue, so they were of no help here. Despite this problem being around for years, TT clearly doesn't have this on their radar. My attempts to get in touch with higher level customer support (those that actually can file a ticket) were futile.
So, I decided to do the following:
Since you can enter quarterly income on form M-2210 if you switch to form view, I initially had put in the correct numbers, got to 0 penalty, and the form disappeared.
I then increased the earlier portions of the income until the penalty ended up being $1. Since this doesn't affect the overall reported income and also doesn't underreport quarterly incomes, I don't believe there's a problem with that. I can live with that one dollar penalty if it avoids having to send in a paper file.
BTW, the machine readable printout of the Massachusetts return will also not include form M-2210 if the penalty is 0. So you'll have to print out the regular form, which requires manual processing of your tax return.
