The option rtcfile in the default config conflicts with runit's stage 3.
Chronyd in RTC mode takes control of /dev/rtc to measure RTC drift.
Stage 3 calls hwclock -w, which messes up chrony's drift calculation.
Furthermore the current chronyd runit service needs the -s option
to effectively use the RTC feature.
See for more info:
https://chrony.tuxfamily.org/faq.html#_i_want_to_use_code_chronyd_code_s_rtc_support_must_i_disable_code_hwclock_code
Switch rtcfile to the rtcsync option, to be consistent with stage 3.
Example config file 1 sets the right options that work out of the box.
So use that example file instead of editing the annotated one.
Example config file 3 will instead be installed to /usr/share/examples.
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