A couple miniature relays, and some simple logic could be used.

Something like this flow should work-
Initiate homing.
Axes move towards home sensors at usual speed.
When first homing sensor is triggered, it powers a relay which disconnects the step signals to that axis.
When second homing sensor is triggered, it does the same, but both home sensor signals are also summed to trigger the IP/M homing input.
Once the IP/M input is triggered, both relays get de-powered.
Homing then reverses the axes, and the process repeats.

Admittedly just stopping the step signal may lead to a bit of an abrupt stop, but you could switch the drives enable signal on the higher speed approach, so each axis coasts to a stop, then switch the step signal on the retract, which should happen at a much slower pace so an abrupt step stop shouldn't be a problem.

For the relays, something like a EC2-5NU (5vdc coil, or EC2-24NU for 24vdc) would work nicely for switching the step signals.
You'd probably need a couple more for the logic, but that with a couple flip-flop type configurations, and independent homing should be implementable externally with the controller thinking it's just homing normally.
If you can't figure out the required wiring, let me know, and I'll add it to my list of things to do.