One thing that's different about both the Warren and the Kitchen Sink incarnations, jc, is that they have ALL been reworked by Eisner (& staff) with gray tones and art modifications. None of the pages is identical to the original printing. So perhaps the "entire contents" is meant to secure copyright over the NEW version of the material that might otherwise be assumed to identical to the earlier versions.
That makes the most sense. It also reeks of (and you've confirmed it as Warren's) boilerplate, so little to no thought of Eisner's ownership probably entered into the contract.
Another factor to take into consideration is that The Spirit Section was a syndicated strip and each newspaper printed it in slightly different format. Some were actual inserts and some were full-page versions that the reader was instructed to cut and fold and trim into an eight-page booklet.
I tried to give some thought to this a while back, but decided that it couldn't matter without invalidating the copyright. What I mean is that one smart-sounding approach is to assume that the strips should be covered by the newspaper copyrights. I didn't know that there were different formats, but that would be another reason to believe that possibility.
However, if that's the case, then every issue actually has dozens of different copyrights. And, since you can't tell which one is "real," none of them can be valid, because copyright law has always demanded absolute clarity. This is similar to the reasoning used against Disney's copyright on "Steamboat Willie;" this is probably valid, because Disney keeps threatening to sue anybody who even discusses the possibility.
So, I do hear you, there, but like most syndicated comic strips, the Spirit would be required to carry its own copyright or none at all.
Also, was it Eisner or Busy Arnold who trademarked The Spirit in 1940?
Oddly, I can't find that. I can see the 1982 mark renewed in 2002, and the 1967 mark. They all refer to having been in use since 1940.
If I had to guess, I'd say that means that the trademark went unregistered until 1967--registered trademarks carry more weight than informal trademarks, but they still "work." That doesn't and shouldn't invalidate it, but it does mean that the trail goes cold, no matter what the story.