yea, I guess you got a point... I wonder how hard it would be to hard-mod it in.
If the MCU (haven't looked at 3DS specs, or frankly 3DS at all for almost a year - whatever chip is responsible for the clock) has a separate input pin for RTC power, then it's relatively easy!
(= considerably harder than the typical nand backup hardmod, but that's because that one is easier on 3DS-except-the-first than average electronic products without testpoints)
You would have to find the trace for that pin (hopefully it's on the outer layers of the board - else
this will be the way 
)
Then, you would need to disconnect it to the board and connect it to your clock battery (through any added electronics, if needed, to provide the right voltage) - fancier variants would use a rechargeable battery and appropriate charger electronics, or keeping the use of the main battery for the clock when available (options range from a diode, as seen on the NES, to a power switching chip as seen on GB/C)
The hardest challenge will probably be space inside the console; of course if someone were THIS dedicated, they could take advantage of this opportunity and make a bottom case replacement with a more confortable shape and all the space for this trick, 18650 battery holder and balancing chip to add a high quality extended battery quality spares for which could be found 30 years down the line, that bluetooth audio transmitter, turbo buttons, full size SD slot(s), capture card....
http://users.libero.it/efa/clock8700.html - This page is not very representative of this hypothetical 3DS hardware upgrade, but shows a semiprofessional approach to the "clock battery only" approach on my family's first cell phone of all things!