That pin should be able to make a PWM signal, intended for backlight control, but you have to be aware of one thing; PWM is not a 96boards low speed signal requirement, the pin on the SoC that would typically be used for PWM, can also be used for conventional GPIO, and that is what it is configured for. I don’t know how to configure the pin as PWM, and frankly, I wouldn’t recommend that you build anything (at least anything commercial, hobby or personal equipment is different) that depends on hardware controlled PWM from that pin. If you did, then it wouldn’t work on a different board, which defeats the purpose of having a universal interface.
Now, if you do need hardware PWM, there may be a reasonably affordable hardware-PWM solution that could work for you; many (most?) very inexpensive microcontrollers have hardware PWM capability. Things like Atmel/Microchip MEGA328 (AVR) and SAMD21 (Cortex M0+). The “Sensors Mezzanine” board, for example, has a MEGA328 and something like 6 or 8 pins capable of PWM. That board is also quite inexpensive ($20): https://www.96boards.org/product/sensors-mezzanine/