I'm opening this bug because I agree with what is requested at T34858: the JS and CSS pages should NOT be parsed as if they were normal "wiki pages" (at least NOT by default, i.e., only if the user opted in for such wiki-parsing). If someone fix that bug, though, the users who create user scripts will have no other hack to track the (crosswiki) usage of their code, and won't be able to notify users about possibly breaking changes in new versions of some JS code.
As you can check on commons:Special:WhatLinksHere/Template:GlobalJsUsage, some people also use fake [[File:UserName UserScript.js]] pages to be able to get a list from Special:GlobalUsage for the associated scripts (see also T3886: A cross-wiki "What links here" (aggregate local iwbacklinks from wikis))
MediaWiki needs a proper way to deal with tracking user scripts.
See Also: T34858: Do not parse .js/.css pages and save their parsed content in database tables