I was a bit surprised as I don’t recall having seen this done before, so I asked about it afterwards. He explained that just like any other time when a kohen is called for the first aliya and there is no levi, the kohen gets the second aliya as well because there is a concern for creating a suspicion of pgam in his yichus. If you ignore the kohen when you should be calling someone from sheivet levi, it looks like the kohen is pasul for some reason. In our case, had there been no kohen, you can call anyone. However, once the kohen got the first aliya and is standing there, he needs to get the second one as well to avoid the pgam problem.
My counter-argument is that this is well and good were it the first aliya of the parsha -- but it’s not. If, for example, you want to add extra aliyos beyond the required seven on a normal Shabbos, a kohen can be called for acharon and be followed by a yisrael, or vica versa, or any other order you like. You don’t have to follow kohen with a levi, and you don’t need to call a kohen twice if no levi is present. Once you are beyond the required number of aliyos, all bets are off.
So here's the chakirah: how do you view the first aliya of the third cycle through Zos haBracha – is it the first aliya of round three (in which case the normal order of kohen followed by levi applies), or is it aliya # 11, one of many hosafos?
The person who offered the psak asked another Rav just to be sure and that person concurred with him, barring proof to the contrary. I needed someone on my side to even the score, so I was happy (it was simchas torah after all) to find the Netziz in Meishiv Davar II:48 (link) agrees with my idea (see the Taz he quotes).