Options for Differential transmission of digital signal
The first thing you should do is specify the acceptable timing error. The solutions to sync within 100ns or 10ps are very different. If you just need to trigger an interrupt within a few cycles in each processors, then differential signaling is unnecessary, a coaxial cable will do the trick.

The two GPIOs solution is risky. If you cannot guaranty that they will start their transitions at the same time, then they will have the same output and the difference will be 0. If the difference is 0, the output of the line receiver is undetermined, and could be rapid oscillation due to noise.

The line driver / receiver will give you much better timing performance, if required. You don't have to be paranoid, differential signals can be very robust. for exemple, LVDS is used extensively in the automotive industry. However, differential signals can tolerate only a certain amount of voltage shift, so if your ground is very noisy you could still have issues.

For synchronization down to a few nanoseconds, over a short distance, and with frequency below 1MHz, an LVCMOS signal over coaxial cable can give good results:







simulate this circuit &ndash; Schematic created using CircuitLab
You can add other protections as needed.

You also need to look at where you are going to input that signal to the microprocessor if you need synchronization better than what interrupts can give you.

If you are expecting ground loops, maybe work at the root of the problem instead and try to minimize the area between your ground connections.