OK, I think I've managed to answer my own question, at least the practical components.
Awhile ago, I bought Spartan and several other movies with the same disclaimer, which I didn't notice at the time. I downloaded the 720p versions of each at the time I purchased them.
I can now confirm that:
a) All of these movies show up in my list of Purchased items in iTunes.
b) All of these movies have the "Download from the Cloud" icon in the Purchased items list.
c) Changing the HD video preference to 1080p in iTunes Store Preferences and re-downloading the movies does indeed give the 1080p version! (Where available, not all HD movies have 1080p versions, some top out at 720p.)
d) I have now downloaded three movies that came with this disclaimer twice each; once at time of purchase and again last night.
At this point, my best guess is that the disclaimer about a movie not being "available in iTunes in the Cloud" has to do with streaming from the cloud to an iOS device or AppleTV. It does not appear to affect re-downloading in other HD formats.
Also, as an aside, I can confirm that the AppleTV 2 (mine at least) will play 1080p content, albeit downsampled to 720p. I saw no stuttering or buffer-pausing. And subjectively, I think the 1080p version looked better—even downsampled.