> You would have expected "/home/kristjan/pydir" since this is the
> apparent directory of the file.

That's questionable.
You usually have the libraries along with the binary: that's for example the case when you do a CPython checkout.

Changing this to not resolve the symlink would break some use cases. An alternative would be to add both the original and target directory if they differ, hoping that there's no conflict in the modules.