It isn't a question of legality. All leases are negotiated on a case by case basis.
The MTA is looking at the presence of Apple as a *revenue stream*. They will certainly increase traffic by a large amount, and the other tenants will reap the reward (as will the MTA through larger returns on revenue sharing at these other locations, -it's not like their not getting some additional revenue with Apple there).
Also, that MTA is a public entity makes no difference. The same forces are at work in the pure private sector. Large companies with a lot of clout, that bring customers and revenue, get to dictate better terms. Kudos to Apple for using their leverage to negotiate better lease terms. It's called business.