My initial comment was that it is not practical to slap a giant 400mm camera lens and camera onto an objective.
As I said, it makes no difference to my set-up whether I use a 135mm or 400mm f/5.6 lens. I've even used a giant white Canon 300 L f/2.8 fluorite lens as a tube lens on this rig (though that is probably near the weight limit). Also, sometimes being heavier actually helps against vibrations. Depends on how the lens is mounted and the frequency of vibrations.
For a color camera I would tend to agree that 3X is a better estimate for sampling frequency for scientific grade imaging. Even if you assume a 3x factor (which is quite frankly overkill for people not making diffraction limited resolution measurements from the imaging data), the maximum array size for a 400mm tube lens in these conditions is 6639x4426 - so you are still oversampling with an S1R.
The Nyquist and 3x criterion apply to monochrome images. Factor in the loss of resolution due to the Bayer array and the number of needed pixels would approximately double. The S1R with 400mm tube lens is not oversampling in this example.
You didn't comment on my main observation. If 200mm is a normal and useful tube lens size for APS, then approx 300mm gives you that same aerial image, with same FOV, on the FF sensor. There is nothing speical about the 200mm focal length except that it gives the nominal magnification on the sensor. Over- or under-sampling can happen with any size tube lens.
with these cameras it just not practical to change out the tube lens when using a variety of different objectives
Maybe this is why we think so differently about the role of tube lenses. In my set-up there is not much difference between changing tube lenses vs objectives. But if it was hard to change tube lenses, again the standard for FF should be 300mm if 200mm is your standard for APS. Why would someone invest in a FF camera if the intention was to always crop the image to APS size?
Using a camera lens as a tube lens will always be less transmissive than simpler optics such as a Raynox or a Thor TTL-200.
This seems nit-picky. The difference in T vs f number for modern lenses is very small, and close-up diopters often have less sophisticated coatings than camera lenses, so the difference in transmission between camera lenses and close-up lenses is usually going to be negligible (and might even favor camera lenses sometimes).