It (the Nintendo firmware on the Switch thats then patched to "create" TX OS.) can absolutely be patched by Nintendo - but Rasa39 is also right, that for example the L+R thing could be changed in response.
That would then be, what I would describe as an "open conlict" between Nintendo and TX.
At its core its really, really simple. Nintendo can break TX OS fuctioning with their next firmware release. At witch point, you won't want to update anymore.
They even could do it - before TX OS even hits most end consumers (those who dont update at that moment- would still be able to use it).
TX "works on all firmwares" is a nice slogan - for about six weeks.
You have to think in core principals here.
Are "online" and "piracy" environments separated (By design, not by people entering Airplay mode)? No.
Does TX have an "independent" - from Nintendo - update channel? No.
Are their modifications detectable by Nintendo, if people go online with them? Yes.
Can you downgrade to a place you have been "before TX OS"? No. (efuses burnt) (edit: Meaning lower firmware. You probably could remove all TX traces - and stay on the current OFW though.)
Will this be acceptable to most people? Probably yes - if Nintendo takes their time to respond - but definitely no, if responses are swift.
So thats the "timing matters" thing.
TX' position at the moment is "bans will always happen", "people probably will be able to update using the games", "online doesn't matter to them", and "they will stay on the latest firmware version we can patch".
Emunand would be a solution with two separate "systems" on one Switch thats not what TX is pushing.
Most of how well people will be able to cope with it, depends on Nintendos reaction. If they do nothing - everyone can celebrate, if they choose to release a new firmware three days before the shipments hit - TX will have a PR disaster. (They are selling you patches which then might not work anymore - "on the most current" firmware.)