Well, up to 125ish MPH, both the 6 and 7 speeds are in 4th gear, so I think that makes them more comparable than 5th to 5th.
Your point on the tire size and roll out distance is well taken too, but so long as everyone uses the OEM diameters, the difference will be negligible. Also, even if they are using different sizes, the effect will be further minimized in 4rth than 5th given the closer startng points.
In terms of determining changes to an individual car, it doesn't matter so long as you use the same gear each time, but I've now seen a few dynos where baselines were taken in 5th and post-modification dynos were in 4th, which led to all sorts of confusion.
Also, I was trying to figure out why all the data I saw pointed to a baseline wtq on a dynojet of around 225 whereas some people claimed a higher baseline of about 240 -- the answer, it seems, is that it depends on the gear used on the dyno.
Someone also recently started a thread asking about typical baseline torque, so clearly it's not just me/us who find this issue somewhat important
At minimum, it means people need to indicate the gear they used at the dyno when posting numbers (which some members have been good enough to do) in order to interpret their results.