Hondata

Is it recommended that gear compensation be set up in most cases, or only if differences are noticable while changing gears? Does the factory ECU change calibrations based on gear selection?

What's the proper way to set up gear comp? I can try to do most of the tuning in one gear and then datalog/make dyno pulls in the other gears and change the gear comp values until everything matches back up (consistant AFRs, no knock, MBT in each gear)...
Is this the right idea?

Also, does the ECU change ignition timing at steady state (like it does for fuel in closed loop), or does it determine spark off of the calibrated tables 100% of the time?

IT is there for those that need it. Some people change the gearing such that it is absolutely necessary.

You have the right idea.

Ignition compensations will have effects on the ignitions values that are modified from the ignition table values.