Data In Polarity register is set unconditionally for all GPIO pins during attach, however its value is valid only for the input pins.
It turned out that above configuration may have side effects on the output pins, which was observed as a boot hang on MacchiatoBin and CN913x-DB, whose PCIE slots' reset signals are connected to the GPIO lines.
Note that it only occurred when booting with FDT (both from most recent U-Boot or EDK2), whereas ACPI is unaffected since GPIO kernel driver remains unused with it.
As a fix remove default configuration of GPIO_DATA_IN_POL register and leave its explicit setting in mvebu_gpio_pic_setup_intr().