Would be nice if they implemented fines as a percentage of profit, maybe a couple months worth of joycon sales or 3% their yearly gross income rather than a vague 35 million euros that does little else than simply acknowledge the flaw.
I heard GBARunner2 tends to be pretty hit-or-miss when it comes to rom hacks, maybe check out GBARunner3 or another emulator if you can get it working?
You probably can for simple asset swaps.
You can modify files you're able to use for USB Loader GX using tools like Wii Scrubber and simply replace existing files with the modded versions. I've had success using this method for plenty of Brawl...