I agree with the original poster. It's not unusual for me to put notes into the Ctrl+E detail fields, some of which are subtractions. For instance, real estate taxes might have a line item for taxes paid through escrow, and an offsetting line item for the portion reimbursed at closing. Yes, my workpapers have the net, but they also have a billion other entries (and the more line-items in the workpapers, the more important it is to have independent entry of the source numbers).

And then there are oddball situations where you have to make an apparently-random entry in order to force the right tax return presentation, and sometimes it's a negative amount. (See also, schedules that don't foot because some sub-calculated number that doesn't even appear on the schedule is a -1, and everyone knows that's zero, so let's just ignore the dollar of loss...)