Is there a simple HW way to mirror the displays, or would it be advisable to wire all to the Arduino and do the mirroring via SW?
I would always wire things up in a 'standard' way and then use the software to make adjustments. More flexibility.
For example, all the row/column adjustments for the LED matrices wiring is done in the MD_MAX72xx library, which allows it to be used with all the LED matrix configurations, unlike most other libraries.