Checking out the CXD5602GG_technical_manual shows that there are a few options for SPR_GNSS_1PPS_OUT signal.
Looking at the schematic of the main board you can track the GNSS_1PPS_OUT signal from the CXD5602 chip on the main board out via the B2B connector to the extension board where it then ends up on something that looks like a test point called CL1. The CXD5602PWBEXT1_part_layout of the extension board will help you locating this point.
Looking into CXD5247GF_technical_manual_02.pdf page 6 will give you and overview of the oscillator/xtal used as RTC source.
CXD5602GG_technical_manual.pdf page 20 shows a table of Frequency tolerance for RTC clock in.
The CXD5602_user_manual page 170 explains abit on the clock sources used for RTC.
Hope these pointers will help you on your way. If not please let me know.