I hadn't realized this until giving it a shot this morning, and I haven't seen this mentioned elsewhere: I've been taking advantage of Safari Reader mostly for reading long form stuff (Esquire magazine has a lot of their classic articles on line, for example). For laughs, while the Reader window was open, I hit Safari's Print button to see if the Reader formatting is what gets recognized, rather than the original page. Perhaps not so surprisingly, it is!
Now it's a simple matter of using the "Add as PDF to iTunes" PDF Service in the PDF Adder collection to add the Reader-formatted page to iTunes' Books category and from there sync to iBooks. Of course, I've been PDFing stuff like this from Safari for awhile, but hadn't thought to try it with Safari Reader. Neat!