As can be seen in the e.g. megaatmega2560 board definition, an Arduino variant is selected through the build.variant attribute. As documented here, you can override attributes for a board definition on-the-fly in the board definition. As can be seen in the builder script, you can override the folder where variants are found through build.variants_dir.
The MCU-PRO_lib.rar gives you the the variant folder for the mcupro board definition (aka, the pin definition). Other existing variants can be seen here.
So, integrating the new variant into PlatformIO is quite easy:
Create a new project for a megaatmega2560
Create a new folder variants in the project folder’s root
Copy the mcupro folder from the downloaded MCU-PRO_Lib.rar into the variants folder