The "Man, lighthouse, city" trio is actually a multi-layered remark that has a lot of meaning to it, not all of which is readily apparant.
1. On the surface, it appears to be a tie together tying the Bioshock Multiverse together, using a meta explanation to show how they're all essentially the same story at their core.
2. It also uses the above point to tie ALL stories together. There is always a lighthouse a man and a city. The Man may be different, the city may be different, and the lighthouse may not be any form of tower at all, but all stories have the same structure. This layer is a meta-commentary on stories as a whole.
3. It's also an attempt to pull the story together at the last minute, trying to cozy you up to the whole "constants and variables" thing. See above point; the forms of the trio can change, but the trio is a set of constants.
The next layers are simply adaptations of the above.
4. All of the constants and variables in Infinite. as you can see throughout the game, literally everything can change between universes. except the three things they had in common; the Lighthouse, Columbia, and Booker. No matter what changes took place in that universe, those constants stayed.
5. The constants and variables throughout Bioshock in general. AFter all, they are all tied to the lighthouse, the man, and the city. While the variables around them changed, the actual constants of the lighthouse, man, and city remain.
6. The constants and variables in all stories, ever. They are all rooted in the man (the hero), the lighthouse (the event that marks the start of their journey), and the city (the strange unknown locale that the hero has to work in).
All in all, it's simply a phrase using easy to identify symbols based on the current story to try to get you used to the whole "constants and variables" thing, which is one of the major points of Infinite, especially the ending.