So my theory is that much of compartmentalization is simply because the search space is so large that people don't end up seeing that there might be a connection between two domains. Even if they do see the potential, or if it's explicitly pointed out to them, they might still not know enough about the domain in question (such as in the example of heavy boots), or they might find the proposed connection implausible.

If a person's knowledge is highly compartmentalized, and consists of these three facts:

1. A human being walked across the moon.

2. There are small rocks on the surface.

3. The moon is a planetary body.

without any educational background, would they choose the right answer?

I believe that their is a high probability that basic intuition would lead to an accurate answer.

So what went wrong, in your case? I don't think that you can attribute it to a failure of compartmentalization. It wasn't that you didn't make connections to your prior knowledge; the problem was that you made too many and that you hadn't organized your priors into a confidence hierarchy.

Confusion occurs when tenuous connections are made and lead to an over-analysis of the question. You differ from the person in the hypothetical, because you had prior knowledge of the forces involved. Connections are only helpful when they are made from strong foundational knowledge to new applications. When you are making many connections from a condition of uncertainty, to a new problem, your intuition fails. It results in the assignment of a low confidence level, to each of many connections, while ignoring basic observations or truisms.

It seems, you were confident in the areas of physics, most applicable in this situation; enumerating the atmosphere, gravity, and mass as the most influential. You attempted to remember how these forces interacted and recognized that they had dimensions to them, that you had forgotten. The connections caused your intuition to be replaced by a humbleness, and the go to answer was a balanced combination of forces. Thus the pen would float.

It is clear that you came to the problem with much more information than my hypothetical person, armed with three foundational facts. You too had those three facts, if that was all that was in your moon compartment the intuition would have been clearer.

(I apologize for the presumptions I made in referring to your thought process. This is a situation, in which, we find ourselves frequently.)