Despite what Tesla is telling you it’s very possible you have a hardware problem with the onboard charger.
The 72 amp charger in that generation S/X is made up of three discrete 24 amp charging boards for a total of 72 amps. It’s not uncommon for one of them to crap out, limiting you to 48 amps. What you describe is exactly what happens when one of the charging modules fails.
That makes sense in theory, but I've got behavior that doesn't make sense. It could be a board, but can 2 circuits do 49 amps? Why would it restrict the amps under what it's capable of, based on a user setting?
Setting the limit to 72 amps at the location, charge will limit itself to 46 Amps due to the higher voltage.
Setting the limit to 50 amps, charge is still limited to 46 amps.
Setting the limit to 49 amps, charge goes up to 49 amps.
setting limit to 48 amps, charge at 48 amps.
setting back to 50, charge goes to 46.
That's reproducible. I use Teslafi logging. The rate was fine before the update, and immediately after the update, it never charged above that new limit ever again. Updates could damage hardware, or recognize existing bad hardware and safety limit on purpose. Wouldn't the SC see an error message it's damaged and the new update now recognized it? The one thing I never paid attention to is if there was any mention of the upgraded charger in the about this car section. It's as if the update removed that I paid for the upgrade 17.28kw and limits to 11.52kw for any setting 50 and over. (The manual over ride case of 49 amps @ 252 volt reaches 12.35kw is what makes me think it's software limited not hardware)