Ray, you are right, but given the depth of field required for this setup I don't think it matters too much in this case.
It matters regarding resolution at the plane of focus. This issue cropped up recently when reviews of the Canon 50D came out. The point was made by many that you needed really good lenses to benefit from the extra resolution provided by the greater pixel count of the 50D; greater resolution than can be obtained with ordinary lenses at F11.
Now the P25 doesn't have a greater pixel count than the 1Ds3 or 5D2, but it does
have wider pixel spacing, a lower absolute resolution in terms of lp/mm (as opposed to lines per picture height), and therefore records image detail at a higher MTF, for any given F stop, than the smaller formats do with their greater pixel density. (Assuming the lenses used are similar in quality, which at F11 they would be.)
Using the same f stop of F11 when comparing cameras of different format would be equivalent to using different
f stops when comparing cameras of the same
What would you say if I were to compare the Canon 40D with the 50D, using F8 with the 40D and F11 with the 50D?
Edit: I should add that it can be perfectly legitimate to compare same formats at different F stops, or different formats at the same f stop, provided the purpose is stated.
If I compare a 40D at F8 with a 50D at F11, it would be for the purpose of quantifying
any resolution difference at the plane of focus, for practical purposes. Can I use the 50D at F11 and get the same resolution (at the plane of focus) as I would get with a 40D at F8, for example? This sort of information can be very useful in the field. At F11 the 50D will provide significantly greater resolution away from the plane of focus (ie greater DoF). That it also provides resolution equal to the 40D at F8, at the plane of focus, makes those extra pixels worthwhile. In other words, I don't have to make a gigantic print in order to appreciate subtle resolution differences at the plane of focus. The benefit is in the greater DoF.