Why install PTP on the AR-150, iirc the AR9331 SoC NIC's don't support hardware time-stamping?
Have you tried https://github.com/mlichvar/pps-gpio-poll with your daughterboard? Unlike the pps-gpio module (which is included in the Linux tree) it doesn’t use interrupts. It uses a high-resolution timer and waits for the GPIO value to change in a busy loop instead.
Could you post some performance numbers of the Quectel vs MTK hardware compared to your older uBlox?