There is no way to customize hotkeys for Joan in fully custom layout.
In the command card for Joan actions like:
Divine Arrow
Divine Restoration
Consecrate
Riders, Ready!
Those actions are hard-wired to the grid layout grid[1,1], grid[1,2], grid[1,3], grid[1,4] and no customization is possible in fully custom layout. It would be nice to have this customization added as I have to go to the keyboard config file to edit those hotkeys.