No, you cannot override the helper files. These are not supposed to be user-facing files. The only files you can override are the view templates (under each component's view/<viewName>/tmpl) and the files under the media folder. These are user-facing files, in the sense that they define how the extension displays (layout). The layout is something which should be up to the end user to customise. The other files define how the extension works under the hood and they are not supposed to be something the user should touch. Simply put, if you would change one of those files the extension is no longer what the developer wrote and they won't be able to provide any kind of support or accept any blame for bugs. Now you know why you can change some things and not some other things :)
Nicholas K. Dionysopoulos
Lead Developer and Director
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