Well, on NYP-BOS per your note, low-bucket Regionals are cheaper for the trips within a few weeks. Also, per your note on WAS-BOS:
-Getting to Dulles is a hassle (it's a ways out of town to the west, and traffic in DC is not always cooperative);
-It's quite possible that you could, in theory, get stuck with a flight one way involving Dulles and the other way involving National, leaving you with an "interesting" car situation;
-For many trips, taking the Metro to Union Station is going to be cheaper than parking at either airport; and
-What are the refund/exchange policies on those airline tickets again? I highly doubt that you're going to get fares that low and 100% exchangability/90% refundability (or 100% pre-printing refundability).
To throw a hypothetical out there, let's do a three-day trip from DC to NYC. Assume a $5 charge getting to/from Union Station in DC (i.e. a mid-cost round trip on the Metro, with transfers available at low cost in many cases). Now, even ignoring the cost of getting to Dulles, that's $30 or so in the economy lot or $51 in the non-economy lot (which involves a shuttle). Right there, you're out a net of $25 to $46. That puts the cost of a cheap WAS-NYP fare up to $90-111 at the airport vs. $85 for the Regional without the special offer. For WAS-BOS, it's $101 for Amtrak vs. $90-111 for the airport. At National, the numbers get even worse (add $6 for the economy lot cost and $9 for the regular lots, for $36/60).
Moreover...how many fares exist at those low rates (and yes, that's a serious question...I don't know)?