Right! But if it didn't, it would save a couple of steps. Which is what this is about... I'm finding Calibre pretty convenient, and now that I have an explanation of the name behavior on the Jetbook, it might be possible to have it work just fine.
Big thanks to both GhostHawk and Kralik for some PMs and what they've answered here. The quote above from the Ectaco forums says it affects .txt, .pdf and .fb2 files. I have a PM that suggests that it doesn't affect or isn't necessary with .pdf and .fb2 formats. Anyone else that can confirm that the naming structure of <authorname>#<title> on the Jetbook only works with text files, and only does what is described above, would be appreciated.
But I think I have enough now to take to the Calibre bug tracker. Here's hoping we can see that naming override go away -- it'll be useful for Jetbook users, too!