"Is it compatible with a HR500 with ATU unit" - YES, at least, it works for me.
What I did, early in the development process, is to get myself another MEGA2560 board (empty) and program it, then keep the original board (with original firmware) aside as a possible step-back. In hindsight I found this was not needed and during the development process (the firmware available now has some changes I made) I would have been able to "step back" but, as said, never required it.
I now simply recommend to upgrade the firmware of the HR500, especially if some of the changes benefit you. I am very happy with 6.01.
73, Geert Jan PE1HZG