Maybe not "fine" per-se. If you have any mods to the car you really shouldn't be taking it to the dealer for anything, and if you do it should be put back to stock as much as humanly possible.
Yes a tune will get rid of the CEL, BUT it will also make your warranty disappear. Frankly, I would just live with the CEL as it is unlikely to cause warranty issues without a tune.
I've actually heart something interesting as of recently. Apparently the early non TU B58's have an issue with scoring the bores. It seems to be attributed to failed fuel injectors that are washing the oil film off the cylinders and it results in a bad misfire.
There should be a manual release under the car. I think it requires an allen wrench and can't be reached without a jack. It is definitely not the most elegant solution.
There is a car that has this done, actually. The Heritage Edition has a hole in the vent and one in the side skirt that apparently does something.
https://www.topspeed.com/cars/toyota/2020-toyota-gr-supra-heritage-edition-ar186959.html
Yes and no. For non-drivetrain related things, the warranty is totally fine, essentially guaranteed. However, for the drivetrain, it gets tricky. If you break smaller items like valve cover or you have an oil leak, those are likely to be covered. Things even up to turbos are consistently covered...
I put a piece of Duck tape. I also clearly told them not to update the car and they had me sign a document releasing liability. As far as I know, they didn't mess with my tape.