The question is though, does the VFS get bypassed if this is put in?
No.
Because scanning for packages isn't slow once the VFS context is
initialized. The time is all within initializing the VFS context for
the jar.
Or, is VFS still used for every deployed jar because of subdeployments?
Yes.
The mechanism you're referring to is jboss-structure.xml.
*
http://www.jboss.org/community/docs/DOC-13178
Even if you use this mechanism, we still need to read into the jar, its
META-INF.
Actually, in MC/AS you never use anything else than VFS to navigate/read
some stuff in file system.
If you do, it's bad/wrong usage. Since that's why we wrote VFS. ;-)