This needs to be addressed. It makes absolutely no sense to have semi-permanent and essential data (e.g. permalink structures) stored alongside temporary data. This "solution" may have made some sense at one point, but WordPress passed that point long ago. The "workarounds" required to clean up expired data should not be encouraged by design. And the fact that use of the options table is only a fallback for a missing object cache is not a reason to let poor design stay unchanged.