So it's another case of socialized software -- thousands of users should pay for a feature that half a dozen people might find useful.  But, to make my question clear, who writes the check to IRS?  The title company that has an EIN?  If that's how it works, then it's not a programming error, it's an IRS error in instructions and procedures. 

A few years ago IRS had a real problem with phony refunds being issued on 1040-NR returns that claimed fantasy withholding.  If IRS won't accept electronic 1040-NR returns claiming withholding that can be matched to 8288 forms, that's just their way of protecting the revenue.  The 1042-S requires an EIN, so don't compare it to the 8288.  If you find another software that allows electronic filing with an SSN, then buy it and tell others where it can be found.