Hi Robin,
I imagine that in Resolve 16 they simply added the warning, as the "Timeline Resolution" really is the absolute resolution, so 'up-scaling' at Render is indeed something to worry about as you've already suffered the resolution loss. I'm not with the Resolve team so if that's contentious I'll leave it with somebody from there to reply.
However, I believe what is going on in your case, is that you're ultimately after 4096x3072, that is 1.33, HD is 1920x1080 1.77, which is 1/4th of Ultra HD, which is 3840x2180, that is 1.77. So if you're expecting the resize operation to track your timeline resolution change perfectly, you should be upscaling your timeline resolution to 3840x2180 from HD such that the aspect ratio is the same, else the resize operation has to 'do its best'. The Cintel Scanner is 4096x3072 full aperture, whereas the actual image area for 35mm formats is never greater than 3840 (by design).
So I think maybe it's just a confusion and nothing actually wrong?
Regards,
James