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It's a workaround, but Troy gave me a hint of using the Terminal to set a hidden preference to force the download instead of rendering within the browser:
defaults write com.omnigroup.OmniWeb5 WebKitOmitPDFSupport -bool YES

That's been working for me. The size of the download is listed correctly in the downloads window. If I change the location preference for downloads, I can store the file someplace other than my desktop.

But I don't like that this opens a blank browser window that remains on my screen even after the download. I suppose that's better feedback than what I was seeing above, but I'd rather just have the download window come up and see the activity there.