I got the matter escalated to a developer, via support, who acknowledged the issue, and has put it on the list for investigation/resolution.
During the feedback I gave support, I noticed this bug only occurs when scaling beyond 200% (with Proteus v3). Like the 270% I used to get a panned view, to get rid of black borders.
I was able to bypass this issue by preprocessing with an avisynth script command, like:
Crop (248, 140, -248, -140)
An exact pre-crop, so a 200% scale will yield a perfect 4K.
Support also said “In the meantime, please use v2, you should not find any advantage to using v3.” So, v2 it is then, for now. Even though I may keep using the avisynth pre-cropping, as it will likely go faster (less raw material to process for VEAI).