Using existing Arduino framework for custom board

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Yes. Both the Atmel-SAM and Atmel AVR platform, to which your SAM3X8E and AtMega2560 belong respectively, have support for a special platformio.ini instruction with which you can re-point the variant folder: board_build.variants_dir. Take e.g. the variants folder of the standard Arduino AVR core, in there are all the subfolders for each board (mega, standard, etc.). Which variant folder it takes is determined in the standard case by the board’s JSON manifest, which has a build.variant value

However, as the documentation tells you, every one of these fields can be overriden in the platformio.ini.

So, let’s say you have a folder my_custom_variants somewhere on your computer (for simplicity sake we say it’s in the project directory), which contains the folder my_custom_mega folder which contains the pins_arduino.h. Then the platformio.ini

[env:megaatmega2560]
platform = atmelavr
board = megaatmega2560
framework = arduino
; set where the folder with all the board variants is
board_build.variants_dir = my_custom_variants 
; change which exact variant to use
board_build.variant = my_custom_mega

will use that custom folder while still using PlatformIO’s standard Arduino core package (in this case C:\Users\<user>\.platformio\packages\framework-arduino-avr).

This exact method has been discussed in the forum multiple times, see e.g. Programm SAMD21 directly and How use a same chip but with different environment？ with the example projects

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