That was fixed in 9d8af78b07976d4d84e0df491abd4e9db848d0ad (February)
by Bernhard Walle <email@example.com> ... if you look at the bug report
associated with this patch, you'll see that rtc-cmos was working OK
with HPET, it's just the legacy RTC driver which got confused after
the recent updates to clock handling.
The story from either Ingo or Thomas (I forget who) was that this is
another case where we have to cope with BIOS braindamage. Not enough
BIOS vendors expose the relevant IRQ routing that Linux could default
to using HPET in what I'd call "sane" mode.
Now, that still kind of implies there could be an option to use sane
HPET IRQ configuration (doesn't hijack RTC and other IRQs, and there
could be a per-CPU HPET) on at least the systems where that IRQ routing
is available. Over time I'd hope that systems like that could become
the common case. But ... someone else would have to do that work. :)