Use different footprint for a SATA connector
Those solutions may work, especially if carefully evaluated. Make sure that the impedance mismatch at the resistor bridges is acceptable and you do not solder the first connector at all, if you add the resistors.

Something that may work even better are cuttable traces. Use CON#2 by default, but replace the resistors with standard traces. Once you switch to CON#1, cut the traces manually. If you are not able to produce a separate PCB for that, I assume that you produce an acceptably low amount of PCBs to justify the cost for that.

An alternative, that may not be necessarily better, adds some cost, but is also more flexible, would be to use a switch:


MAX4986
Pericom
...


With that solution, you could use both ports, without ever having to change your process.