Great question. In my opinion, yes, for a couple reasons:
# First, I agree that going up and down is going to take longer.
# Second, any recommendation for a timed ascent–in meters per hour, etc–should be qualified by the angle of the terrain. The most efficient angle for trained athletes seems to be within 14-16 degrees (25-30%). In contrast, a typical staircase is usually 32 degrees (62%). Boxes in gyms are even “steeper”.
Your rate of ascent for box stepping will depend on the height of the box. If it’s a typical box from a gym, it’s almost certainly going to be steeper than what’s most efficient.
For example, to achieve an angle of 14 degrees (25%), your step need be only 4″ high… If you climb 3,000 4-inch steps, you’ll have your 1,000′ at 25% (1,000′ ~=~ 300m). You can imagine how much faster your cadence would be on a 4″ step than on a much larger step or box. For example, the sustainable cadence on a 4″ step is more than three times that of a 12″ step, thus making the vertical ascent speed faster overall.
# Personally, I would use a treadmill for this test to make it predictable and repeatable. Unfortunately, most treadmills only go to 15%. But if you can find a gym with a Woodway 4Front or a NordicTrack Incline Trainer, you should be all set. The 4Front goes to 25%, and the Incline Trainer goes even steeper.
Most importantly, regardless of the angle, be consistent between tests and, because of the variables, ignore the results of other people. Person to person, results are unlikely to be comparable unless done on the same “terrain”, whether that’s outside, on a box, or on a treadmill.
I hope that helps.