The runspeed enchant can be quite significant on movement fights for bot the mechanics and also DPS. If you get to a spot 1 second faster you're getting an extra second to DPS, which means an extra 50-90k damage right there. Given the number of movement fights, the DPS gain from going with the runspeed enchant is better than going for the slightly better itemization.
Let's go on the low end of things and say 40k in that second. If the better itemization gave 100 dps then it would take 6 minutes and 40 seconds for the better itemization to be equal to the runspeed. Chances are you're going to move more than once during the fight though, so that extra DPS time really adds up and could go past 100k, which means you'd need to spend over 16 minutes in the fight. How many Patchwerk fights have there been that lasted that long? None. Stick with the runspeed and make things easier on yourself and your raid by being quicker.
There are a lot of "ifs" and "buts" in this classic debate, but it boils down to the fights themselves. I doubt anyone is craving 100-150 DPS so badly that they are going to swap back and forth boot enchants between high and low movement fights.
Pandaren's Step is a 9% speed increase (10% with Death's Advance activated), which if you run for 5 seconds, will give you .45 seconds more to DPS. 50% of a GCD...if you have available resources Obliterate (~60k) or Frost Strike (~35k) (most likely no KM if you're moving). In a 7 minute Patchwerk fight, the Haste enchant (more like ~150 DPS) would net you ~63k damage.
My recommendation is that if you spend more than 10 seconds running towards the desired target (trying to get into melee range) in a specific encounter, it is worth having the Pandaren's Step enchant.
But if you look at the current tier, how many fights would this be the case? Appears to be less than half.
Possibly a small increase in overall damage, but not enough for me to drop the utility of the minor run speed improvement.