I am headed for exactly the same approach.
I’m currently on an SKR board, with Marlin, with the LowRider’s X and Y swapped.
I also have a Jackpot board, with FluidNC, and will be doing the X-Y swap whenever I go to install it.
It should be easily doable.
For purposes of remembering what is involved, here’s a link to where I made notes on doing it on Marlin:
The software / firmware changes were all regarding endstops and homing directions.
Those kinds of changes in FluidNC should be easy. I have not yet done it so I cannot comment specifically on the “how” just yet.