That's because those PMOD ports are connected to FPGA pins which can be reconfigured (inside the FPGA) for a lot of different functions/protocols while on the microcontroller those are wired to peripheral pins that only have a limited set of hard-wired functions. On an FPGA board you can make a custom design and be able to literally connect 4 different I2C devices to 1 PMOD port and have 4 different SCL and 4 different SDA lines (you'll need a bunch of wires but whatever). Basically you can customize those PMOD pins however you like/want/need.
