Yeah, I never got why the various episode guides and such counted both parts as one episode. One story, sure; but it's definitely two episodes. It even aired on two separate weeks.
Evidently it was counted as one episode in the original production numbers. The production numbers for "The Menagerie" are 6149-16A and 6149-16B, so officially both parts were counted as episode 16. I guess the numbering conventions in Hollywood were different at the time, or maybe it was a Desilu convention and Paramount used a different numbering system.
Which raises another question-- could "The Cage" have even happened to Captain Pike in this timeline? I'm not sure of the date that it took place, but it seems with Kirk now being in charge of the Enterprise during the time that Pike originally had been, it might end up happening to Kirk instead.
"The Cage" happened in 2254, which would be about a year before Abramsverse Kirk enrolled in the Academy -- at which point the Abramsverse Enterprise
would've still been in the early stages of construction. So it's conceivable that Pike could've gone to Talos IV, but it would've had to be on a different ship.
Of course, these comics are playing pretty damn fast and loose with the timing of these retold stories, putting them in 2258 or so even though the Prime versions happened in 2265-7.