If you acquire a NTSC Earthbound rom and flash it to a japanese cart thats basically piracy right? Because you don't own a copy of NTSC Earthbound. You could however own a cheaper copy of Mother 2 that so happens to be flashed/modded/hacked with a fan translation which I think would be technically more legal and cheaper.
So you only want to patch the japanese rom to use a fan/'free' translation, and not touch the official english language rom because you want to sell the real english version.
Ok, that is going to severely restrict yourself.
You could also just dump your roms, and have them all on one single flash card.
Sell the original carts if you want.
If you cannot live with:
a) having a 'real' flashcart
b) dumping your own carts, keeping the roms and selling the carts
c) simply downloading the roms aka piracy
then in all honesty I think you need to lighten up

I'm not advocating piracy, I'm not telling you to. I'm just trying to explain/show that you are making things very difficult for yourself.
I have a 3rd party flash cart for gameboy, and also some official nintendo ones (gb memory) that i reflash and it's great. very cool to use the original hardware.
It's moral issue that doesn't sit well with your religion?
Or something else? I'm curious and not trying to offend.
which I think would be technically more legal and cheaper.
this is never going to go to court, no laywers, nothing.
there's no reason to even consider what is 'more' legal.
But of course, there's always the slim chance of the police searching your house with a warrant:
Maybe they thought the soldering iron you bought (to solder this chip you want) was used being used to manufacture explosives or something.
As they break down the door, they just so happen to see a Japanese nintendo game in your snes, but the text on the tv is in English...
They look into it further, then ask you what's going on, are you a hacker? is this a fraudulent game?
They take you in for questioning.
It's good cop bad cop.
Good cop asks you what games you like.
Bad cop slams the desk and demands to know how you obtained this special cart.
Being scared, you sing like a canary. You explain you bought a japanese game from ebay, the english version was too expensive. You dumped the japanese game, and found a free fan translation. Even though the game had a western release, a team still translated it anyway. Then how you patched the rom you dumped with the free translation you found online. You then explain how you bought a chip some guy made, to redirect the data from the original rom to a custom one you can program. Then you flashed the patched rom to the chip and that's how you have it. You tell them it's all legal, you didn't break a law.
It seems to go well, and they put you back in the cell for a few hours whilst they do some paperwork, and you get released on bail.
A while later new evidence comes in, the free fan translation was actually fake, the team just dumped an early leaked version of the final english rom and so all the ips patch does is simply convert the japanese version to the official english rom.
Next thing is you're doing 25 to life and sharing a cell with a guy called bubba.