It looks like there are very few ways to synchronize the WUT counter to other time bases, but does anyone know if WUTWF could be used for that? The reference manual says that:
WUTWF: Wakeup timer write flag
This bit is set by hardware up to 2 RTCCLK cycles after the WUTE bit has been set to 0 in
RTC_CR, and is cleared up to 2 RTCCLK cycles after the WUTE bit has been set to 1. The
wakeup timer values can be changed when WUTE bit is cleared and WUTWF is set.
It sounds like the flag changes state at the next RTC clock edge after a full RTC clock cycle.
And I wonder if that's the case, is the edge the same that triggers the interrupt.
If that's true too, then the synchronization should be possible within ~100 ns by polling the WUTWF when the processor is running at 80 MHz.