There are papers arguing that smoothies aren't as good as eating real fruit because it seems that there's actually a benefit to having to break down cell walls, even at the expense of not getting 100% of the nutrients from it. However, cooking food breaks down cell walls, although obviously not to the same degree. It's not clear that breaking down cell walls is harmful, even if it's not beneficial.
A lot of ultra-processed foods have been accused of having unhealthy levels of certain ingredients (usually sugars or salt) and certain styles of cooking can add harmful compounds.
It would seem reasonable to say that there's a band at which a given ingredient is beneficial (analogous to a therapeutic threshold), with levels above that being increasingly harmful, eventually reaching a recognised toxic threshold. In terms of the harmful compounds from cooking, it seems reasonable to suggest that, below a certain level, the body's mechanisms can handle them without any issue, that it's only above that that there's any kind of problem.
So it would seem that we've got three factors - processing that can decrease benefits, ingredients that follow a curve that reaches a maximum before plunging, and processing that can increase harm.
Nobody wants to be given a complicated code that they need to look up, but it would seem reasonable that you can give a food a score out of three, where it would get 3 if you get maximum benefit and no harm, where you then subtract for reduced benefit and increased harm. That shouldn't be too hard for consumers, most people can count to 3.
Yeah, understood, food is going to vary, since it's all uncontrolled ingredients and processing itself is very uncontrolled. So take two or three examples as a fair "representative sample". Further, most manufacturers can't afford to do the kind of testing needed, and our understanding of harm varies with time. No problem. Give a guidebook, updated maybe once every couple of years, on how to estimate a value, which can be used, but require them to use a measured value if measured, where the value is marked E or M depending on whether it's estimated or measured.
It's not perfect, it's arguably not terribly precise (since there's no way to indicate how much a food item is going to vary), and it's certainly not an indication of any "absolute truth" (as we don't know how beneficial or harmful quite a few things are, food science is horribly inexact), but it has to be better than the current system because - quite honestly - it would be hard to be worse than the current system.
But it's simple enough to be understandable and should be much less prone to really bizarre outcomes.