I don't feel like renaming the package or the module is the right thing to do.
agree, it's not.
I could work around it by installing a symlink, or by replacing
autopkgtest-pkg-python with my own customized version.
symlink is not correct, replacing is what i typically do.
Would it make sense to patch autopkgtest-pkg-python to allow overriding the
autodetected module name (perhaps using a user-defined control field)? I
would be willing to write a patch if enough people think it's worth
doing.
I think this is nice feature, please go ahead :)