I haven’t tried it, but I don’t think you would have a problem using those pins on a Mega 2560. From the schematic, only d2, d4, and d9 are being used, since the Mega uses the ICPS pins for SPI. d3 would be free, as long as you haven’t changed the INT jumper from d2 to d3.
I’m using a Mega 2560 with this shield myself but only to get a 2nd UART for GPS.