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To my knowledge, as I had to research a bit about how E+ treats gap years for some simulations, your understanding is correct.
First, here is a really old post that talks about it, just to add information to the subject: https://onebuilding.org/archive/energyplus-support/msg00012.html
You asked, "it shouldn't hurt to always set it to yes, right?" The answer is yes, as you have to go out of your way to simulate a gap year: The .idf NEEDS to have the runperiod on a gap year, the gap year data has to be in the .epw and the flag set to yes. If you simulate the runperiod on the .idf as 2019 for example, the gap year won't be simulated nor affect the simulation.
"What if I'm exporting January data, or May-September data?" then, as long as the .idf does not try to simulate days that are not in the .EPW, the gap year flag won't affect anything.
Good luck making your tool and I hope you can share it here once its done!,
PMP