It fits in the outline of the module. More important in the GW-48T02-1 and such since those are often down in a carrier (e.g. in Sun systems), but I do have some systems with devices very close to the RTC module where a CR2032 in a holder wouldn't fit. I did a lot of measuring to settle on the largest standard coin cell I could get in there.
There's also a height restriction on some systems (some of the PS/2s, many of the Sun systems). The CR1225 was the best overall solution, and I'd rather only have to buy one kind of battery holder. It's also the cell that was present in several of the different kinds of modules I disassembled for the design phase of this project, so it should provide comparable life to a factory module, discounting of course cheap cells with poor seals (I think it's Mostek that claimed a 50% increase in cell life due to the potting compound making up for poor cell seals). To avoid the problem, I just order high-quality brand new Renata cells
They're $0.85 each in QTY 1 from Mouser.