Quoted By:
I like to play on the 3/DS anyway, but I play once on the physical cart for "I wanna transfer up to HOME eventually" as you said (though moreso Bank desu), whilst any replays that won't be transferred to future games, namely enhancement hacks, are either from a rom on an SD card or emulated on PC.
I like the latter especially since the NSO SNES controller for Switch is perfect for DS games in all ways but the touchscreen, given the quantity of buttons is the same except the Switch one having ZL/ZR for potential macros or other functions like speed-up or pressing somewhere on the touch screen.
Emulating on PC is also better since you can speedup for grinding purposes, which is good for the Johto games or B/W1, or any of them really, so replays aren't a slog if you have other stuff to do.