Add a $config['plugins']['locale_path'] which can be set to override the individual plugins' locale subdirectories.
This will apply to *ALL* plugins in *ALL* languages, so should probably only be used when doing site customization...
Edit that (make sure you at least set the CHARSET, probably to UTF-8) and save your customized .po
files into the structure as above, and use msgfmt to generate .mo files for final output.