There's two tunnels to the airport. The "local" I'm guessing in this instance was probably the Sumner/Callahan tunnels (Route 1A), with the express being the Ted Williams Tunnel (I-90), the newer tunnel built in the 1990s. Certainly agree that at that hour they're likely a wash time wise, but at certain times of day they can vary a lot. The distances are short enough that you're not talking about much of an issue either way in the pre-dawn hours.*
*The only caveat I can think of is that sometimes the airport exits themselves are very backed up at key flight times (like when people are arriving for the early morning flight push). I have seen instances where there's a backup in the Ted Williams for the airport exit, and at the exit off 1A. One advantage to 1A is that there is another exit just past the main airport exit where you can double back to the airport pretty easily.