I went ahead and pulled both throttle bodies. I took some pictures for comparison.
In the first picture, you can see the similarities between the throttle position sensors. They're the same plug with the same colored wires in the same order on the harness side.
S14 on left, S13 on right:
In this picture you can see the differences in the pulleys. You can also see the cold start control mechanism that is present only on the S14 TB - at least that's what I think it is. I didn't look it up because I don't really care.
S13 on left, S14 on right:
Here is a view of the bottom. You can notice that the S14 TB has two vac/boost ports coming from the TB. I don't recall what they went to - again, don't really care, just observing.
S13 on top,
S14 on bottom:
Here is the view from the front - this is when the differences are really apparent. You can easily notice the difference in size between the two throttle bodies. A 10mm difference doesn't seem like a lot, but it's noticeable and substantial. I'm not sure why Nissan went with such a tiny throttle body on the S14.
S13 on left, S14 on right:
This picture shows the back. I was surprised to see the notches cut out on the bottom of the S14 TB. When you look inside the intake manifold plenum, you can see that there is a pathway [for lack of a better term] from these notches to the #1 runner. I'd be interested to know why they did this and what the philosophy is behind it.
S13 on left, S14 on right:
I put the S13 TB on the S14 plenum to make further comparisons. The next picture is a side view. This shows the first few problems. For starters, you can't bolt it up because the coolant line hits the #1 runner. Also, where the throttle cable would attach to the S13 TB in this orientation would be near the 7 o'clock position which might be too far for the cable to reach.
The view from the top illustrates the other problem. The bracket that holds the throttle cable is not in line with the correct pulley. This could potentially cause some binding issues with the cable if adjustments aren't made. I suspect that the bracket will need to be hogged out to allow it to better angle to the pulley.
So my conclusion right now is that the SR20DE throttle body would indeed be the better option. I might try to find one so I don't have to ruin a perfectly good S13 TB. After all, I do have intentions of using the S13 SR at some point in the future.
Hopefully others will find this comparison useful.