Please note rpi-eeprom-config -e is always replacing the bootloader version with the default one which may be different (older) than the bootloader currently installed (active). And the default is linked to critical (at least in current LE 11 Nightly).
I don't know if the same happens in RPi OS or if it's LE specific but I am not sure that's the best behavior (at least for users preffering the stable or beta bootloaders) as the wrong bootloader config may be applied (some newer options may be unknown to older bootloader).
Maybe some check and warning to the rpi-eeprom-config script should be applied when the current and further bootloader versions does not match.
LibreELEC:/usr/lib/kernel-overlays/base/lib/firmware/raspberrypi/bootloader # ls -l
total 0
drwxr-xr-x 2 root root 92 Nov 24 18:25 beta
drwxr-xr-x 2 root root 92 Nov 24 18:25 critical
lrwxrwxrwx 1 root root 8 Nov 24 18:25 default -> critical
lrwxrwxrwx 1 root root 6 Nov 24 18:25 latest -> stable
drwxr-xr-x 2 root root 92 Nov 24 18:25 stable
LibreELEC:/usr/lib/kernel-overlays/base/lib/firmware/raspberrypi/bootloader # ls beta
pieeprom-2021-10-27.bin recovery.bin vl805-000138a1.bin
LibreELEC:/usr/lib/kernel-overlays/base/lib/firmware/raspberrypi/bootloader # ls critical/
pieeprom-2021-04-29.bin recovery.bin vl805-000138a1.bin
LibreELEC:/usr/lib/kernel-overlays/base/lib/firmware/raspberrypi/bootloader # ls stable/
pieeprom-2021-07-06.bin recovery.bin vl805-000138a1.bin