Multiple ground planes, single point ground, and a level shifter
I'm thinking tie both sides of the level shifter to the input ground and have the output current take a long path through the single point ground?

I would do the opposite, so keep the loop at the output short because that's where the current flows.

The inputs are high impedance so almost no current flows. For noise reasons the argument could be made that the inputs should have the better ground connection but since we're dealing with digital input signals, I would not be too concerned about noise at the inputs.

I think in the end there isn't that much difference between ground at input side or ground at output side. This isn't RF, not very sensitive (using low voltages) and also not high current.

If you still have doubts you could consider to connect the levelshifter's grounds to a local ground plane and then connect that plane via a link / zero ohm resistor / blob of solder to the output side or the input side.