Why do Star Wars sets include the Disney logo/brand name while Marvel Super Heroes sets do not?
I emailed TLG:

These changes are different as it is how Disney would like it be displayed.  Prior to a set release, each set goes through a number of reviews.  One of these, is our designers show Disney the boxes for them to sign off on and approve, after they review the boxes.  For each set, they said the boxes were approved for release!
It does appear that for the Marvel, they were ok with the Disney Logo not included on the exterior but they did want the Disney Logo on the Star Wars sets!

I also talked with a customer service representative. He took ~5 minutes to &quot;do research.&quot; Here's a portion of (only) what he said (comment and ping me in chat if you want the full transcript):

I'm sorry, but we don't have a clear answer on why the boxes differ. What we do know is that the designers create the artwork for the boxes that the sets come in [sic; in] and after that the parent company (Disney) signs off on the designs!
That's it exactly! We provide the images to the parent company and they do have a say in what appears on the box, once we get the okay from them we print them off. With the Marvel and Star Wars TM they were both approved, but have the different printing.

He suggested reaching out to Disney. Unfortunately, I am still in the process of doing so.
What the above replies mean is that (1) designer decided to design a box a certain way (possibly for aesthetic reasons), (2) Disney approved the design, (3) this is the design you see on your boxes. As such, there is no &quot;real reason&quot; the boxes were designed this way.
I will be updating the answer with a reply from Disney.
The (second) reply from Disney; the first was a generic &quot;thanks for the feedback&quot;:

That is actually a good question for LEGO- there is a contact page in the links you sent us.
This is not something we could answer...