The Wikipedia reading list plugin seems to be introduced to allow users to add Wikipedia articles to their reading list when browsing Wikipedia using one of the supported web browsers. The fact that the plugin allows users to add articles from non-Wikipedia wikis and some Special: pages from all wikis is contradicting it's main goal as a Wikipedia Reading lists plugin. This should be stopped. IOW, the plug-in should not allow users to add pages from non-Wikipedia wikis or Special: pages to their Wikipedia reading list (at least not NOW). There are several reasons for this.
1. Possible confusion
The feature is named and advertised as Wikipedia Reading lists. There is no statement in the project page itself stating what pages the users can add to the reading list using* the plugin. The fact that it would allow users to add pages from other wikis could puzzle and confuse users given that it is a Wikipedia reading list plugin. Further the apps (at least the Android one) doesn't seem to be supporting pages from non-Wikipedia wikis completely. See, App issues.
2. App issues
Lack of clarity of source wiki
The source wiki of the page being shown is not clear or incorrect for non-Wikipedia wiki pages. For example, in the Android app every page has a 'Wikipedia' footer and licensing information. The same footer is shown for pages from non-Wikipedia wikis (that's possibly because they didn't anticipate users could open non-Wikipedia wikis in the app ;-) This might cause issues (possibly legal ones) when non-Wikipedia pages are shown in the app with that footer.
Screen shot of footer shown for a Commons user page
Screen shot of ambiguous entries in Reading list
The two User:Kaartic entries are not redundant. They are user pages from two different non-Wikipedia wikis. It's not clear which wiki they are from even if you open the pages.
Lack of complete support
The apps don't load or behave correctly for all the pages that the plug-in allows the users to add to the reading list. For example, I add a MediaWiki User page to my reading list. The following is a screen shot of how the app responds when I try to open it.
The following is how a flow board page is shown.
Most (if not all) of the links in non-Wikipedia wiki pages shown in the app prompt the user to open the browser which might confuse the user given that a page from a non-Wikipedia wiki is shown in the app.
3. Special: pages issues
The plugin should not allow users to add Special: pages to the reading list as it goes against the meaning it conveys by it's name (reading list). Further the apps don't seem to support Special: pages either. For instance Special:MobileDiff directly tries to open it in the browser. That might not be useful.
Conclusion
So, it would be nice if the plugin does not allow users to add pages from non-Wikipedia wikis and Special: pages for the time being.