There is a lot of logic here which is good in a vacuum - the problem is when it gets applied to the marketplace, and 30 firms with 30 different revenue functions.
1. The Red Sox do not have the same fiscal constraints of other teams. If they place those shackles on themselves, it is entirely by choice. The value Lester (or anybody) provides does more for the Sox bottom line than it would in Tampa.
2. Jon Lester is very hard to replace because of both the quality and quantity of production. There is no way they can replace the quantity of production with one pitcher next season. Indeed, it is unlikely that any of their pitchers, regardless of age - will produce the innings value that Lester will provide in the next 3 seasons. He is basically one roster spot which has to be replaced by 2-3 pitchers in his absence.
3. You have to eat some suboptimal years to absorb a premium free agent. The question is what those years look like and can you live with that. With Lester, you'd probably get 3 years where he is more like (on average) 2012 Jake Peavy than a Cy Young contender. But that is 1200 innings of #2/3 starter production ... and in the way the market has evolved, that is probably worth $20-$25M a year fairly.
4. There is a possibility that this front office just does not believe in compensating players to that degree - which sounds good until you see what they are charging the public. It does not compute in a tolerable way.