Travis,
The collector should be hotter. Why?
Initially, your first "blast" out of the #6 exhaust port will be hotter when starting up the car. However, as the car heats, 2 exhaust pulses will be hitting the collector. (That assumption is predicated on header design however) The Law of Heat Conduction says:
H=-kA dT/dx where...
H=Thermal energy transfer rate, -k=thermal conductivity of the element, A=cross area, dT=change in temp, dx=change in temp over the area. (dT/dx=temp gradient, it may be easier to think about it like that)
Basically, the less the temperature gradient, the less the transfer rate. Since exhaust pulses are hitting the collector in a much more regular pattern than the relative sporadic pluse from the #6, the amount of energy transferred into the collector is greater, and since there's less of a gradient, the heat tends to remain. (vs the #6 runner where it will cool off)
Now, if you had the perfect EGT gauge with incredible resolution (and eyes to read it

) you would see the pluse is slightly hotter than the collector as it cools in the runner. After all, when have you ever applied a heat source (exhaust pulse) and heated the object above that of the source?
In practice, the collector becomes an average of all exhaust pulse temperatures. As with any average, the more pulses, the worse the resolution. For instance, if #3 detonate for a few revolutions, it may only appear as a 20 C degree jump at the collector. Of course, if you're probe is on #6, you wouldn't see anything. Likewise, if the #6 were detonating, the probe in the #6 runner may change ~80 degrees C and you may actually be alerted to the problem.
Ok, that was clear as mud. lol