The Settings Addon can only hold a limited amount of different settings. We simply cannot put every single setting for all supported hardware.
A specific, and separate addon for e.g. Raspberry Pi would be an option. PR's for such addons are welcome.
I know that hdmi_rotate works on my 2nd monitor, but I never had to use lcd_rotate. You sure you have "lcd_rotate=2" in the config.txt, instead of "lcd-rotate=2" ?
LibreELEC works with 2 seperate partitions, the system and the (data) storage partition. What do you need the /boot folder for? Your config.txt file is sitting in the /flash folder, which you need to change to "rw" if you make any edits/changes.