@michaldybczak
We do not control how another plugin author adds to his code. We can't make them follow proper procedure. If they choose to edit code without making an update they can, even though WP discourages that. Having said that, this is not a wordfence issue. We get new versions when the plugin author releases a new update and store it in our repository to do comparisons against. We also give you the ability to compare the changes with the original and ignore them if you find it to be something the author slipped in at some point. You can also choose to update your plugin with a fresh copy since ours should have the current code and yours, since there was no real update issued, will not.
I'd suggest you talk to the author f wpsso and ask why they are making changes outside an actual release.
tim