Your point is well-taken regarding challenges faced by lenses on 45mp cameras, especially those with older designs like the 600G. However, I don't agree with your conclusion that the Nikon 600E, or the 400E and 500E for that matter, are not capable of excellent sharpness and outstanding images, even when used with 45mp cameras. Yes, all things being equal, a quality lens with a 4,000 imatest result would be sharper than one at 3,500. But 3,500 is still a high performance level and significantly better than that of a Nikon 200-500.
I do wish you had chosen to provide links to your sources, as the narrative by the testers that goes along with the numbers is important. I'm assuming you're basing your numbers and statements on Photography Life reviews. Below is an excerpt from their review of the 600mm f/4E in which they state how impressed they are with the sharpness of the lens despite being tested on Nikon 45mp D850.
https://photographylife.com/reviews/nikon-600mm-f4e-fl-ed-vr/2
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"Lens Sharpness and Contrast
If you have previously used a high-end 600mm f/4 lens, you already know what to expect – these lenses are designed to be remarkably sharp. But how much better can new optical designs be compared to their predecessors? As it turns out, quite a bit better. Since many of the older lenses were either designed for film cameras or did not take into account digital camera resolution, they tend to have more optical aberrations and quality control issues that can impact lens sharpness on a modern high-resolution camera. In comparison, modern lens designs are optimized for high-resolution sensors in order to deliver much higher levels of sharpness, and they go through much tighter quality control. As a result, sharpness differences in images are fairly obvious.
Let’s take a look at how the Nikon 600mm f/4E FL ED VR performed in our lab. Here is an MTF chart that shows the lens performance at different apertures, as measured by Imatest:
While a detailed comparison to other lenses, including the 600mm f/4G ED VR, is provided on the next page of the review, one can immediately notice how sharp the 600mm f/4E FL ED VR is, even wide open. I was surprised to see how sharp the lens is when shooting on the 45 MP Nikon D850, which is quite a demanding camera for any lens."
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I thought it would be interesting to note that ephotozine's imatest on the Nikon 600mm Z reveals a 4000+ score, demonstrating the benefits of the most recent design.
For those seeking the highest performing 600mm lens in the Nikon line, the 600mm f/4Z would be it. But IMO, for those seeking an excellent 600mm lens at substantially less cost, like the OP, they couldn't go wrong with a 600mm f/4E.