Mind telling my how a patch based OS replacement should work?
I mean TECHNICALLY it would be possible to load up a different OS from A9LH, but that would require you to do a whole shit ton of reversing of the current system fw, patching calls to get certain methods to run. And most of that would have to be done assembly based at some point.
Have fun creating bytecode patches that let you turn the 3DS OS into i.e. a Linux OS. It's near impossible.
The Linux PoC you're talking about is running an OS from the 3DS OS. it's not a replacement. It's more comparable to a VM.
To make this easier to understand.
It's TECHNICALLY possible to turn your webbrowser into a game, by patching the program (with for example a Debugger), but noone would even attempt it because it doesn't make a lot of sense and is a lot of work to get done.
Running a game in your webbrowser however is not that difficult, you just need to adapt whatever you run to whatever the Browser can run.