@jan is exactly right. The developers work hard to try to maintain backwards compatibility so the hook we have in the plugin should live from version to version.
One of the best things about WPeC is the plethora of hooks and filters that it has to change the behavior. You just have to be willing to dive in and identify them. If someone wanted to learn the code base I’m sure there would be an opportunity to help create more accessible documentation for the community ??
The other reason for keeping the changes separate is that if you run into a WPeC technical support issue the first thing you would want to do is disable all extraneous plugins and see if the the issue remains a problem. As soon as you change something in the code base all bets are off as to if someone will be able ( or willing ) to help you diagnose the problem.
For each future version you upgrade into you will want to do a really quick check to be sure the formatting of the notice and the processing is OK.