I'm pretty sure something is wrong with the firmware I downloaded. I flashed the 3/5/21 version of Marlin firmware from https://marlin.crc.id.au/ and it is somehow working better with the LCD firmware (which I got from TH3D), the Z offset is working as it should, and the leveling process has more points and goes faster.
After changing your firmware, you always need to overwrite the old values in the SRAM and EEPROM with those from the Firmware. Which you do with M502 & M500:
Installing firmware does not by itself alter the EEPROM, so these settings needed to be seeded into SRAM via M502 and then saved into EEPROM via M500.
You could also run a G-code ...
There are multiple ways to achieve this:
You don't necessarily need to do that in firmware, TH3D is based on Marlin firmware and is just a monolithic implementation for most popular printers and boards that helps novice users to easily configure their printer, but in the meantime it hides other options from plain sight.
Being a derivative fro ...