Some forms match specifically (such as your W2s) but others aren't filed with your tax return and 1098s are one of those. As long as your total interest reported doesn't exceed the total interest that the IRS sees on your return, then there isn't an isssue. Even then, there probably isn't an issue since not all interest is reported on form 1098.
IF they were forms where the specific data was transmitted from each form to the IRS then it would be a different story, but they're not. Only one number goes on the tax return - and that's the only number the IRS computers will see no matter how you enter it into the software. What matters is what is on that final 1040 and its schedules, and the number of 1098s or whose is what isn't on there - just the amount of interest.
As long as that amount is accurate, you have nothing to be concerned about. There is NOTHING to audit about HOW you enter the data into software programs, it is the data itself and where it ends up on the tax return that matters. This workaround gets the right number on your tax return, the only thing that matters.
