I’m not familiar with Chrony. With NTPsec, the PPS driver docs say [0]:

> While this driver can discipline the time and frequency relative to the PPS source, it cannot number the seconds. For this purpose an auxiliary source is required;

And so (with NTPsec), you need to define two sources even though it’s coming from the same device. One for the PPS signal for clock discipline, the other for the clock value.

> refclock pps ppspath /dev/gpspps0 prefer

> refclock nmea baud 57600 prefer

0: https://docs.ntpsec.org/latest/driver_pps.html