If a `uname -r` was used as a variable in a dep file, then those who make custom kernels would have to make module extensions that correspond to what is available in the repo. It wouldn't allow the choice of just leaving your custom kernel modules in your initrd, or as one large extension which I imagine the majority of those with custom kernels use one of these two approaches.
I think you are correct in that users of custom kernels do not package the modules according to the same structure as has been done by the modules for the standard kernel, but I would gladly package according to that structure in case that allowed me to automatically gain the benefit of the dependency information.
I can't think of a way to not have module extensions load when another kernel is being used aside from removing module extensions from dep files and instead mentioning the dependency in the info file. Though that would help those with custom kernels, it would be punishing the majority of users. There are about 32 dep files that contain kernel module extensions, and though that is not a lot, it would affect the experience of using TC to not have module extension dependencies resolved as is present.
If the loading tools looked for the string "2.6.29.1-tinycore" in the names of packages when loading and just discarded to load such packages if `uname -r` returned something else, then that would help users of custom kernels and others would be unaffected.
/Lars