Sadly indesign does not distinguish between application specific and document specific preferences in the preferences dialog box. Some can be set for application like display setting and some cant be.
also if you dont want the notice(you mentioned), just click on "Dont show again" checkbox at the bottom of the warning dialog box. Henceforth you wont be notified. This is document level setting and can changed from preferences->general if u ever Want to revert.
give this page a read for a detailed list of application or document specific preference:
hopefully this answers your query
Oh, sorry I was unclear, I am aware of the differences, the settings available, and that I can turn it off, which was supposed to be my point—just supposing it were possible to turn it off for this FILE, but not the application. So my question (I'm sorry it wasn't clear) was mostly rhetorical, or meant to be read as a feature request.
There are many settings that are document-specific. As far as I know "Don't show again" is not one of them. It is application.
According to your link (thank you!) there are just these:
Use Typographer’s Quotes (Document)
Automatically Use Correct Optical Size (Document)
Apply Leading to Entire Paragraphs (Document)
Smart Text Reflow options (Document)
Character Settings (Document)
Units & Increments (Document)
Color – Margins, Columns, Bleed, Slug, Preview Background (Document)
Snap to Zone (Document)
Guides in Back (Document)
Minimum Vertical Offset (Document)
All other options (Document)
That link from Bob Bringhurst is from November 5, 2008, so it is now eight years old. It's not bad, but there is a better one.
Mike Rankin updated his illustrated guide and it can be downloaded as a PDF from InDesign Secrets. It's for CC 2014.
You can be a free or paid member. It looks like this download is for either. I am a paid member, so I can't check for sure. I put a screen shot below.
Pro Tip: It is worth joining as a paid member!