I suspect it will impossible to process Wiegand on the M-SoM (RTL872x). The problem is that the GPIO is very slow, slower than the pulse width of Wiegand, so even with interrupts it will not be able to process it.
In some cases, like Neopixel, the SPI peripheral can be used to generate timing sensitive pulses. It also can be used for input. Since Wiegand requires two inputs (clock and data), it would require using two SPI peripherals, which is probably not practical because it would be difficult to synchronize them, even if you had two available.
What I would do is use an inexpensive coprocessor (PIC, STM32, etc.) to convert Wiegand to UART serial. You can optionally use Asset OTA to be able to remotely reprogram the coprocessor. As an added bonus you could use a 5V tolerant 3.3V coprocessor so you wouldn't need the level shifters on clock and data.
Thanks for the guidance. But why did you use a processor with weaker GPIO? We have now used the GPIO on Argon, Boron, and B524, with no problems what so ever.