Understood. This would require patches to linux' hctosys.c systohc.c rtc.c rtc-proc.c, rtc-snvs.c, rtc-dev.c and a standalone re-implementation of hwclock to avoid patching busybox's hwclock.
What I'm not sure about though, is how to interpret the value of the lower bits in the SNVS_LPSRTCLR register that get shifted out by the linux rtc_hctosys (and not set by systohc)
any help you can give me there would be much appreciated. The fact that it's 15 bits and we have a 32kHz oscillator is suggestive, but not sufficient.