It is an ever so slight downhill after the first few miles and while you gain a few seconds possibly on that -1 percent grade, you also have to take time away for that dark one mile tunnel you run through early on with a headlight, and deposit said headlight after the tunnel with a bib labeled bag in a collection box after the tunnel, and actually running on gravel is also slower. Is it a fast course? Sure, but it is not so simple to just look at the elevation. I ran at a very similar pace a year earlier at a much hillier race until my meniscus tore, and just this year (right around the time when Boston was meant to be) ran 38:57 in a 10k, so me running 3:17:23 at the Tunnel Marathon is not that extraordinary.
I mostly picked that race for the scenic location, and because I do prefer running on gravel versus asphalt or cement.