[Conclusion]
Mismatch python version between /usr/bin/python and flatpak's python causes this error.

[Story]

Privately developped python script uses numpy library works fine with flatpak's gimp.
Updated flatpak's gimp.
Above script starts giving error with No module named 'numpy.core._multiarray_umath'

[Solution steps]

Check python's version under /usr/bin and flatpak's bin by the followings.
/usr/bin/python3 --version
Python 3.10
/var/lib/flatpak/runtime/org.gnome.Platform/x86_64/45/active/files/bin/python --version
Python 3.11.0rc1
Install python3.11 by apt
Reinstall python libraries such as numpy

[Main cause]
Since numpy's _multiarray_umath is a cpython built library, require reinstallation under python3.11.