I used the ATMega2561 because I have them and I spent a few months designing an application specific board for it. I didn't use a Mega2560 because it won't fit in the case, the huge amount of jumper wires tends to make it unstable in an RF environment, and the TFT LCD display I have is setup as an Uno shield. I didn't buy 2560 chips because they were 10 to 15 times more expensive and the TQFP64 package was not supported at that time-it seems to be now. I did not fee like routing the TQFP100 package, nor did I need all the extra I/O for this project.
Seeing as I provided the 2561 port assignment, the Uno Shield pin number, and the Megacore pin assignment number, yes, you can look and see what pins I am using for the data bus on my 2561. All the pins are used as digital IO lines, so I fail to see why what I've done won't work once the code understands which pins to use.
As I stated, the library was obtained from Adafruit's Github some time ago. The newest library adds some extra dependencies for pin mapping and registers. Even after updating the library, the code as presented still compiles and runs. The issue is that in the new pin magic.h, which seems to be the way to change the pins, the code is commented on what it is doing, but not how it does it. I am not familiar enough with what I am doing here to be able to see if I can, or how I can, rework or add a new pin assignment to support my hardware.
Since god invented shields, maybe you can show me where to find a shield designed to live in an RF environment, that contains three TWI controlled flexible clock generators with low phase noise, high stability, and wide operating range; two high IIP3 mixers, a multi-mode demodulators and two multi-mode modulators, switchable bandpass filters for both IF and RF sections, and a 30W PA?
There is a reason I'm using what I'm using, and going through the extra work to get it to do what I need.