Also to add to Am's reply.

the difference in DOF @ f/8 between a 100mm lens and a 105mm lens is minimal, to negligible.

The lens itself may(will) have light transmission differences(to other lenses of similar types) .. ie. T-stops.
So while the Zeiss may be @ f/2.8, it's T-stop could be something like f/4(don't know .. just an example).

Also, as lenses focus closer and closer, you will get focal length shortening. Very few lenses don't do this nowadays.
Some of those lenses can also misreport the real aperture value as you focus closer, others will report the actual aperture value.

I remember that Canon's don't adjust for aperture as you focus closer, Nikon's(and AFAIK) most third party lenses do(not sure about Zeiss)

So for the Canon 100/2.8 if you focus to MFD the camera may still indicate an aperture of f/2.8, where the reality could be something like f/4.8 or so.
The Nikon 105/2.8 will display the physical aperture(ie. I think f/4.8), even tho you haven't adjusted it at all.

if you have the Nikon, it will go down to a small as f/57(at MFD) and will stop at f/32 at infinity.

At f/8 you probably won't notice this, but at wider apertures vignetting also has an impact on the intensity of the light through the iris and onto the sensor.
So two lenses at f/8 may not produce the same (overall) exposure because the resultant image is affected by various degrees of vignetting.

So(to answer part of the question), in theory two different lenses set to the same aperture with the same scene(eg. say a plain white wall) should produce the same exposure no matter the focal length. This assumes no vignetting and the same T-stop from both lenses(which can happen).
of course in real life you don't shoot plain white walls, and it's almost impossible to get the same framing from two disparate focal lengths(ie. 70mm to look the same as 200mm).

One of DxO's strengths as a review site for lenses is that they test for T-stops of the lenses when they test. it gives you some idea of the differences you may get in any exposures if you're using the same camera/lens settings across different lenses.
To answer another part of the question, although not directly ..

Don't use f/40 on the Nikon 105VR!!
I meant to say Don't use f/40 if you value sharply rendered fine detail!
I've used f/32 which is about as far as I'd stop down, but the images require a fair amount of USM/highpass/sharpening of some sort to recover fine details.

(Haven't yet tested the 105VR thoroughly on the D800 yet to see how low I can go with aperture .. did my tests on the D300 early on(ie. years ago).

As to the DOF from the Ziess compared to the Nikon .. it depends.
It depends on how the Ziess is designed. If it reduces focal length as it focuses closer and doesn't report that, then the comparison is hard to judge without physical testing.
We know that the Nikon 105 does both report AND report an accurate aperture, so with that in mind you can easily test with side by side comparison images.

Something to note. The Ziess doesn't focus down to 1:1 as does the Nikon. As I don't have any experience with it, if the Ziess lens extends considerably as you focus closer, then the likelyhood is that it doesn't reduce focal length. But it may still not report an accurate aperture.
Also with the Zeiss lens(es) some of the older version don't have CPU chips on them, the newer ones I think do(well they do for Nikon) .. this could make a difference in the the way that the aperture is reported to the camera.

I think that from about 3 or so meters almost all macro lenses begin to report the physical aperture value(ie. it starts at about f/3 or so).
So to compare the DOF of each from 3 meters at f/8 or f/16 could be a bit hit and miss. You could be reliant on personal opinion as to how each will be rendered considering that the lenses may be mounted onto different camera brands .. ie. different sensor types.

I probably confused you more than helped .. if so ... sorry!