For this section, it wasn't just the IRT building it, but rather the Dual Contracts, which included the BMT, which also runs through this section, and has that opening visible to 7th Ave. station in this area (where it's level wit hte Brookly bound local track, and the express tracks have gone below). All six tracks were built together in a common structure, so you have to take into consideration that as well. I don't know if there were any provisions for more BMT tracks, but it is likely just extra space to support the rest of the infrastucture; or could even stem from a time when it wasn't decided which portions of the new construction the BMT would get and which the IRT would get (lke there had been talks of IRT getting 4th Ave.)