Boron RTC not retaining time after System.reset

IIRC there is no need for special treatment to keep the RTC (on Gen3 devices rather a RealTimeCounter than a RealTimeClock) persisting its count across a mere reset.
About this portion of the docs

See information on Backup RAM (SRAM) for cases when RTC retains the time. RTC is part of the backup domain and retains its counters under the same conditions as Backup RAM.

This only means the same rules apply, not that the user needs to store the timestamp in retained memory.

However, to properly enable the retained memory it should be executed inside the STARTUP() section as shown in the link. Just calling that function from outside setup() will fail to build.