First, thanks for this comparison Rob, always informative. I hope the southern autumn is treating you well in the windy city.
There are of course many technical issues, let me run through a few - but first, the FE55 image is very much superior. More lively, more information, better definition, clearer (less muddy), more micro-contrast, better tone handling, more accurate, just to mention a few characteristics.
The zoom image looks almost like a watercolor, you can get some back with judicious sharpness but not enough to matter or change things. The FE55 is a seriously great lens. Even among high end normal primes, and detail is its long suit.
caveats: I'm not a (modern) zoom fan. They are 'over-cooked' in design terms, too big a range, and too uneven with strong centers and poor outer frames. No real 3D image depth. Made for pros!
Technical
. the crop is just off the magic center 'donut hole' of each image, at an image height of 5-7mm or so - this will favor the zoom significantly.
. f10 hurts both lenses badly - the centers fall off a lot. If you were looking at outer frames and corners, it's less important but for this crop, f5.6 is best, and in fact if you want smokin' centers with still very good outers, use f4 for the FE55. It gets out of bed early! lol. The zoom is also better at f4-f5.6 in the centers.
. 55mm is near to the best FL in the zoom, it would lose badly to many primes longer but especially wider. It's horrible at 24mm, like so many are.
. downsizing, raised above, probably matters less here. I'd use PS to get to the final comparison size, downsize on pixel count in 50% increments using bicubic (smooth), for the first 1-2 steps, then for the last d/size to the final file size use bicubic (sharper). [This is straight from the horse's mouth - Jeff Schewe. It works.]
. the big gain is the camera/sensor tech, maybe as much as the extra sensor resolution, I'd say. Any SLT cam is disadvantaged and then no AA enters the picture, but you get a refined look instead.
You would see what the zoom is capable of if you stuck the lens on an LA-EA3 (not EA4, the SLT again) on the a7rII. This might be good or it might be bad news for the zoom! 36/42mp has a habit of ordinarying (TM to me) many, many lenses better than the venerable 24-70/2.8, again in the outer reaches more than centers.
I have both the a99 (my partner uses it now) and the a7r (mk 1). You benefit from higher res sensors, even at post-diffraction apertures, even f22 is better than many wider apertures on lower mp cameras - strange but true. [This is from Zeiss.] The a99 gives up a stop of high ISO from the SLT but not too bad. A very fine camera, nevertheless, great EFCS and 'thunky' shutter. Strong. Many of my best images were shot with it. Let's say we are not in a rush to replace it.
The a99 (and RX1) was Sony's first iteration of its great new age sensors, and it works really well with great lenses. Well 'of course' you say, but it gets a huge boost from my Zeiss lenses, which do not need to maximize acutance to give you excellent images, a fine balance between contrast and color and very even cross-frame performance do that for you. I'd back the CY 35-70 to easily outpoint the ZA 24-70/2.8 at 50mm, and absolutely crunch it at 70mm.
24mp works best for slightly less demanding stuff - street, people, arty shots, close range, contrasty (it has very good DR 'below base' ISO, try 50 for better results - Sony knew the SLT robbed IQ, so they boosted low ISO some). 24mp is not at all bad, it's just less good than 36/42mp where in your face IQ matters.