“What exactly is the benefit of setting it in gear?
I always set the in D idle rpm, the timing, and the A/F ratio with the tranny in D and with the brake applied. I have found that tuning an auto in D will require a richer A/F ratio, which in return gets me a smoother vacuum reading, and a cleaner take off (no hesitation or stumble) from a stop.
I also run an idle solenoid so that I can set my in D idle rpms differently than my N/P idle rpms. I like to keep my N/P idle rpms lower than my in D idle rpms which helps with keeping the engine from dieseling when it is shut down. The higher in D idle rpms makes sure that my alternator is excited at a stop (keeps the load off the battery when using brake lights, turn signals, wipers, etc.), and I like a little more rpms for a solid lifter cam at idle.
I usually have a second person sitting in the car with their foot on the brake after a major combo change to allow the tuning to go a little quicker. But after that is when I will just pull into a parking spot to reference the in D idle/vacuum/A-F ratio when I am away from the garage.
If I need to make an adjustment, then I just put it into P and make my change. Then after I make the change, I put it back into D to see the results.