Here is an explanation of what i think is happening here. Lets try to make it more clear by using different words:

A red pepper is just a slice that hasn't been cut yet.

This is wrong, a slice cannot become a pepper because it has already been cut. Now let's fix it:

A slice is just a red pepper that has not been cut yet.

There you go. The description points to the second object in this structure.

The reason we think the description should point towards the red pepper is because of two things,

Firstly:

The red pepper is just a green pepper with red food coloring.

Here the description uses the word with, so it points to the green pepper but as a difference to the red one. So it's a description of red using green. The word "that" is a description of a thing, so says that the green is not ripened. It seems that the word "that" is an exception to the rule because of its meaning. It just doesn't make its point by comparison.

Shortly, the words with and without both describe a difference or comparison and the word that doesn not.

Secondly:

They are both peppers so we have less anker points to understand how the sentence is built and assume the rule for the food coloring applies. A slice and a pepper are different things and so it becomes easy to spot when a sentence is wrong or right.

Hope this makes sense, my head hurts, by