One thing I should note is that when looking at prints (at least for when it comes to technical analysis) being able to see accurate representations of the lines is far more important than the uniformity of colored regions. Color is almost always at the whim of the printer on any given day, whereas the black lines (from the keyblock) should always remain the same. Granted you're going to have issues either way (using this tool or doing normal scaling) as the source material is inherently compromised.

Although it's not clear what scenes exactly the upscaler was trained up, I suspect that it's currently best suited towards scenes that have lots of large bold lines and not lots of tiny details.