One of the things you can do is check the fuel trims. First, before dynoing, check the long term trims to see how much the DME is adding or subtracting fuel based on your baseline. These trims get applied during open loop as well. When on the dyno doing a baseline, check the short term trims, which can tell you what the DME is doing right now. They should be zero or close to zero. Then, after the mod, in closed loop operation, check the short term trims. After a mod, they should change, adding fuel because you should be bringing more air in. In theory.
This is overly simplified and there are lots of fuel trims and they get applied in different ways, but it's one way to check. It also doesn't tell you about timing... and obviously if you flash the DME, this method won't tell you anything useful.
Personally, I think that same temperature Vbox runs on the same stretch of road after a few tanks of gas is probably more useable data.