Yes, if you move the plugin into your project’s directory, any changes you make there will not affect the main plugin.
A caveat - when you try to package your project, you’ll get an error if the plugin exists in your project folder AND in the engine folder. The only workaround I’ve found is to temporarily remove the plugin from the engine folder and replace it with your project folder’s plugin. This seems to be an oversight from Epic, so if anyone knows how to stop the plugins from conflicting with each other, I’d love to know the solution.