Originally Posted by JSWolf
When this plugin is used, does Calibre do any modification to the ePub other then the function(s) of the plugin being used? For example, removing the page-template file and links, is the ePub the same other then these missing things?
That is exactly the ethos of this plugin. It does not use any of calibre's conversion pipeline code, nor does it do any css or html parsing/rewriting.
So if you choose the xpgt files & links option for example, the only change that should be made is to the opf file to remove the reference to the xpgt, the xpgt file itself will be deleted, and then on each html page that had a <link .../> it will do a simple raw text regex based replacement of just that.