Once done, can it be copied onto an SD card and played on the 3DS?
I'm gonna suggest tentatively yes. I didn't have any problems running the Tales of Innocence fan translation on 3DS on my flashcart.
If you're running TWLoader/TwilightMenu to launch directly from the SD card you might have problems. The ToI fan translation didn't run for me there, crashes on the intro video. Though SRT OGS: Endless Frontier does work fine with TwilightMenu, so it's a toss-up I guess. If you're in doubt, get a flash cart (R4i 3DS Gold I think is the standard one, you can use the R4 Wood firmware).