lintian currently emits a tag for cross-compilers because they make a directory in /usr's top level for TARGET i.e. /usr/m68k-linux.
The FHS states: No large software packages should use a direct subdirectory under the /usr hierarchy. An exception is made for the X Window System because of considerable precedent and widely-accepted practice. This section of the standard specifies the location for most such packages. bug 33251 has discussions from various people on the topic. What I would like is policy to either codify current practice or come up with a reasonable practice the cross-compiler maintainers will be willing to work with.