When I applied for my ID last November (still waiting...) it was certainly the case that we needed to apply for a green book before we could apply for a Smart ID - that may not be the case any more (in which case I'm envious!), but it's worth nothing that only a few Home Affairs offices are still able to process books - when I applied it was Belville, Caledon or Malmesbury, so I went to Belville.
You're quite right that they verify your marriage again for the ID (yes, even though they have just done it for your PR permit), and this sometimes takes some time, for reasons only known to Home Affairs. Realistically, given that there is an expectation that all PR holders apply for an ID, it's a mystery to me why they don't issue the ID at the same time as the permit, given they already have all the relevant information, but here we are.