The tag is present in Lintian version 2.104.262. That is the most recent version we know about.
Packages using the X Window System should not be configured to install files under the /usr/X11R6/ directory. Debian has switched to the modular X tree which now uses regular FHS paths and all packages should follow.
Programs that use GNU autoconf and automake are usually easily configured at compile time to use /usr/ instead of /usr/X11R6/. Packages that use imake must build-depend on xutils-dev (>= 1:1.0.2-2) for the correct paths.
Refer to Debian Policy Manual section 11.8.7 for details.