This is a floating deck to be supported by ground screw anchors. There is space for 2 x 6 joists in all but one area where the ground is elevated and not enough clearance for a 2 x 6 so I'm wondering if I could use a 4 x 4 for this one joist. The elevation consists mostly of surface tree roots that cannot be disturbed without possibly killing the tree so I am very reluctant to shave off 2 - 3 inches of roots so the 2 x 6 will fit.
A 2x6 is almost 70% more rigid than a 4x4 in the vertical axis. A 4x4 might not provide enough rigidity.
If the clearance is that important an issue, use a single metal beam for that location. You'll be able to find a an appropriately rigid box-sectiom beam that is small enough.
Alternatively use several 4x4s to replace the 2x6.