Logic fault.. concern over self-compiled binaries do not mean..binaries outside of the packaging system.
The nautilus situation is worth explaining.
nautilus as packaged requires gvfs-fuse. fuse has a versioned dep on the kernel. You can compile your own kernel...and package it as an rpm which still satisfies the packaging dependences for fuse or any other package which directly depends on the kernel. There are only a handful of packages in the Fedora repository which directly require the kernel package. And in each and most cases its a minimum kernel version specification. nouveau being the only different one.
For the F-10 release set, not including updates we have:
repoquery --repoid=fedora --whatrequires --alldeps kernel
Note that in an update a new varnish was packaged without the kernel dep so on an updated Fedora system that's 8 packages which directly require a kernel package to be installed which claims to be better than the minimum version.
The real problem in the discussion isn't whether or not self-compiled kernels are being considered. The unspoken question is this, is there a better way to expose specific kernel settings in the packaging deps so that people generating their own kernel packages known exactly which options are required to keep functionality working. Obviously a kernel can be compiled without fuse support, but we don't have a way to express whether fuse is available in a packaged kernel or not. So as a result the very weak dep on minimum sufficient kernel version is used. My personal take on it is that these deps are somewhat historical artifacts which were introduced to make updating would work as expected when a new feature was added.