Since Armando's chapter 18 only describes one way of using the PSR to help you create your story, I think you can certainly diverge from his method in whatever way feels appropriate. So one answer might be to just do what feels right or natural. You could hit on a couple of the PSR variations in scenes for one encoding, then another scene might incorporate two encodings and one PSR variation, etc. It would also depend on the length of the medium. In a long novel I would think that sometimes more than one scene might hit on the same PSR variation.
I think the language of the PSR itself is fairly vague because it is pretty open -- you just explore the signpost's Type in terms of Variations A, B, C, and D. It doesn't even say you have to follow the order.
Also, I kind of feel like the PSR is the "icing on the cake" of the story's narrative. It can help you create a great story but too much icing isn't always a good thing, so if you feel the need to ignore it or diverge from it, I think that's fine. Just my two cents though -- I'm no expert!