Capaldi will probably stick around for about 3 seasons, I imagine Moffat would leave around then too and we'd get a new Doctor and new showrunner who would then have a few seasons themselves to tell the story of the thirteenth and final Doctor and what comes next (if anything comes next.) Of course, if Moffat didn't leave then, he would be the showrunner for the 13th Doctor and would be in a position to tell the Last Doctor story he so clearly wants to tell.
No -- Capaldi is the 13th Doctor. He's still numbered as the 12th for the reasons Gaiman explained in the above quote, but he's the thirteenth life of the Doctor, because there was one we didn't know about until now.
You're missing my point entirely. It's not about the numbering system now that we have a secret Doctor, it's that we shouldn't have. The "one we didn't know about until now" was a bad idea and only created so that Moffat come up with an excuse to make Matt Smith the 13th and final.
Matt Smith should have been the 11th Doctor and 11th life, Peter Capaldi the 12th, [insert future Doctor Who actor here] as the 13th, No secret Doctor we didn't know about, and the 'no more regenerations' storyline should be handled years down the track when we get to it and only by Moffat if he's still the head writer that far in the future...