As long as the air filter is clean, I can't see why you would sync without the filter? You drive with the filter in place, so it seems logical to make sure they are in sync with the filter fitted...
I always did it with the filter fitted. Never gave it thoughts, but you indeed want it to run well with filter fitted indeed. Suppose the air is not distruibuted evenly with the filter(s). Still the throttle valves would compensate for that, and the engine would run well.
With the filter off, you can however tell if any big synch issues are there, when lifting the slides manually and looking at the butterfly valve openings (any clear difference). When the engine is not running of course. So you could do that check beforehand.