Yes, of course you can do that. Just for the Launchpad the numbering is always done on the boarder of the PCB = Pin Headers of the board, as this is the point where a typical user would connect something.
If you prefer for your own board to have the device pin numbers used - you can do that.
Doing the updates as you mentioned above should do that 🙂
To get the board in the GUI you need to
- add a device in the variants folder - as just discussed with the update of the pins_energia.h file
- add a section into the boards.txt file (located in the folder above)
in a section the name before the dot needs to be identical (all lines need to start with that) and this name needs to be unique
So take the existing MSP430F5994 part, replace the name before the dot and the name = display name in the selection drop down menu