Something like Nintendon't is actually already happening on the 3DS. I recently confirmed and did a bit of documentation on the 3DS' ARM7 CPU, something we previously thought was implemented in software on the ARM11. The 3DS actually has all the hardware for the DSi AND GBA on board. That means it's got 3 CPUs, up to 6 cores, and 3 GPUs. Crazy thing.
It's kinda funny - that means the GBA VC is the only virtual console to not use emulation.
Running DSi stuff outside of TWL_FIRM is kind of a crapshoot. It's better to just bear with having to boot back into your modified firmware than try and get around that. Oh, also don't downgrade TWL_FIRM. You could have some really weird stuff happen, and it won't actually do anything for you.