Disclaimer: The PDF results of either Scrivener 1 or 3 are not suitable for publication! Not even close. This is a writing program, not a book making program. For that you need an entirely different kind of software. I suppose at the very least a word processor, but even then, those are more tuned for writing than design as well.
(side question: DOES 1.9 support gutter margins?)
It does not, and while v3 does, it isn’t something I’d ever mess too much with outside of giving yourself a way to create generous outside columns for notetaking, on proofing copies.
That said, you won’t find those kinds of margin settings in the Page Setup panel anyway. There is no need for that tool, it is just where you change the paper size, and compile settings can change that as well (although I don’t know, if your print setup is crashing Scrivener it might not work in there either, I don’t know what could cause that, the print setup dialogue is coming from Windows as I recall). Well, you might as well try one of the “Paperback” compile Formats, as they do have alternating margins already set up.
But again, I agree with the above, it is better to compile simply, to stylesheet-drive text and import into a layout tool for all final formatting. Even though I say simply, I think crash learning the compiler, even just to use styles, in a text that was never written with them (v1 had no styles), immediately, to get out an overdue copy is maybe too much? Maybe just get the text out in v1 like you’re used to, and start plugging away at it in a DTP or similar.