Well, most probably you can’t use 2 USB for direct connections.
From this documentation of extension board i understand that it don’t have any USB, you must use CAN-FD connection for that.
CAN is not present in RPi, so you would need additional CAN-FD<->USB board.
Ok, but I think it’s overkill to add second Duet3 board to just get additional steppers.
I would try to utilize not used pins from 9 additional IO ports which Duet3 6hc board have, also most probably there are many additional pins which will not be used and can be utilized.
Then I would use dummy external stepper driver boards to get additional steppers which would be driven by single Duet board.
Multiple-mcu configuration is working but sometimes it have some restrictions, From my point of view single controller configuration is always better.
There seems to be some confusion here. “CAN-FD” is a protocol that is a superset of the “CAN 2.0B” protocol. Some micro-controllers (such as the SAME70Q20B) have hardware that supports both the “CAN-FD” and “CAN 2.0B” protocols. Klipper supports the CAN hardware on the SAME70Q20B - one can use it both in CAN mode or “USB to CAN bridge” mode. Klipper will only send “CAN 2.0B” messages through that hardware, but that does not adversely impact the support.
To the original question here - it is possible to run Klipper on the “duet3 6hc” board. However, I don’t know if Klipper can run on the “duet3 3hc” board. In order to use Klipper it would be necessary to flash Klipper on both of those boards.
At a quick glance, the “duet3 3hc” board uses a micro-controller family similar to supported chips (the ADSAME51N). So, it may be possible to run Klipper on it with no or minimal code changes. At a minimum, though, one would still need to track down all the pin mappings and create a config file for that board.