The Mass Apply Credit window is not part of standard GP as far as I'm aware although I do vaguely remember a 3rd party that has it (maybe Willoware?). What you are describing makes sense though. If no date restriction is used then the tool is probably checking all documents in the apply open table (RM20201) to see what all it can apply.
The only reason I could think of to not use just today's date is if any transactions are coming in from a previous date or post dated. Maybe using a week/month range would be more efficient to make sure nothing is being missed.
It does sound like implementing the Paid Transaction Removal tool on a routine basis wouldn't be a bad idea also.
