The mpremote utility expects to find the .config/mpremote/config.py file relative to the path stored in the XDG_CONFIG_HOME environment variable first, then looks in the HOME environment variable next if that was not defined. ¹

In Windows, HOME is not an environment variable defined by default, but the counterpart is HOMEPATH.

I am currently able to work around this problem by manually creating a HOME env var and setting it's value to %HOMEPATH%, but if the mpremote utility could be updated to either check the OS first and then use that to determine the appropriate environment variable, or use the suggestion in this StackOverflow answer ²:

from os.path import expanduser
home = expanduser("~")

If you're on Python 3.5+ you can use pathlib.Path.home():

from pathlib import Path
home = str(Path.home())

to correctly find the user's home directory, then support for user-defined commands would be enabled for all OSes.