For purposes of theory, Yes. According to Dramatica, as far as my understanding goes, it’s theoretically impossible for one mind to be able to build a comparison of all the states (items of a quad) completely individually. When working out this comparison, you have to use one as a baseline. Which one you choose may depend on context, but you can’t remove this choice.
For purposes of practicality, it almost doesn’t matter. The idea presented there will end up in your writing if you are using Dramatica, anyway.
This particular variation of your question is actually a bit more difficult, and the analogy I used, as presented actually breaks down. As such, I’ll be working purely with the theory this time. In the following, I’ll be using a Main Character with a Concern of Obtaining.
The Concern of a throughline is a Type, but because it is a Concern, it is seen throughout the story, from beginning to end. For example, in the hypothetical, the MC deals with conflict from Obtaining from start to finish. Every act will reference Obtaining in some way. In addition, since Obtaining is made up of Approach, Self-Interest, Morality, and Attitude, the same story-length struggle can be broken up into the six pair-wise relationships between these Variations. Note that these comparisons specifically target and explore the Concern of the MC from the start of story to the end. This is how you can get the three act perspective.
However, we can also view the story in this way: Since the MC is dealing with conflict in the Physics Class, she will need to pass through some conflict from each Type under Physics, one at a time, to work out (or fail to work out) whatever personal issues she has. For this, let’s say the order is Understanding -> Doing -> Obtaining -> Learning. Thus, we are now looking at four acts, each of which corresponds to a single Type. Here, we broke a Class down into its Types, but we can do something similar with each Type. We can break each Type down into its four Variations. In this case, the Variations don’t belong to the single Concern of the throughline, but they will be shaded by it.
Both of these views will give you a story. More interestingly, in the first paragraph, the six relationships will eventually give you some static view of the four Variations found throughout the story. In the second paragraph, you’ll eventually find that you create relationships, though you didn’t deal with them directly.
In other words, everything ends up tied together.
From a practical standpoint, which paragraph you choose to use for your implementation depends on how you think and write.
Personally, I need to plan with the static points, and fill the transitions and relationships in as I write. (I use the second paragraph.) However, I know of other writers who actually have to plan the movement that they wish to write and let the standstills show up. (They use the first paragraph.)
Strictly speaking, though, Jim’s answer, as quoted above, is probably the best view to take.