Looks like a change somewhere in the recent kernel stuff. The Kbuild modules_install ends up creating files of modules.* (symbols, alias, dep, *map) in the $IMAGE/$DESTDIR location, and then collision-protect triggers when that stuff is about to be copied over. This is only a concern for ebuilds that use the Kbuild modules_install instead of the linux-mod_src_install. Converting them to the linux-mod_src_install would be a pain for cases with lots of modules. Probably add a special function to the eclass that removes the files, and just update the ebuilds to call it.
I think the modules should use linux-mod_src_install, and if it's too hard then we should fix or document the eclass more. This is not the only thing that will go wrong if they work behind the back of the eclass.