If you use a package that depends on pyside2, then you might be stuck. You could try building pyside2 with a modified PKGBUILD. This seems like a bug/difference in behavior with paru: https://github.com/Morganamilo/paru/issues/1377
If you're adventurous, you could use another package management tool. Not familiar with garuda though.
Or maybe wait until paru developers possibly change their tool, or the AUR package happens to change to work around paru behavior?
Do you have an example of the incorrect metadata external ids if they are set? And what is the format of the files that was midentified?