Money is just a representation of resources. It will take a lot of resources to build this ship compared to others that are not as fast or better.
Starfleet launched six Galaxy-class starships on ten-year missions with something like 75% of their volume empty for future expansion. And then during the war, they sent out the rest even emptier than that. Starfleet is not above throwing money around even if it may not be the most economically efficient allocation of shipbuilding resources. And raw material, manpower, and engineering aren't the only things to go into starships. Or in the real world, for that matter. Look at how people continue trying after decades to make an aircraft that flies as fast as a plane but can also hover, despite how intractable the problem has been. Considering that reversible saucer-separation is a proven technology in Trek, it seems a lot more defensible that Starfleet's designers would try taking a shot at attaching a third separable section, and making them all more independent.
To use your earlier model, the choice between three 33-point Defiants or three 30-point-equivalent thirds of a Prometheus seems like more of a fair trade-off if those Defiants will spend most of their time at a starbase waiting for a Defiant-worthy job to come up, while the whole Prometheus can also (or, more likely, will mostly) do jobs that are suited to a larger, more versatile ship.
(I'm suddenly imaging the Prometheus pitch meeting taking after the original iPhone announcement. "We're here to show you three revolutionary new starship designs. One, a trio of stripped-down, combat-ready escorts capable of outflanking any enemy. Two, a medium cruiser with a focus on tactical missions, but still fully equipped for peacetime exploration and patrol. And three, a high-speed command ship capable of coordinating an entire sector and getting to trouble spots faster than anything in the fleet. A set of escorts, a next-generation medium cruiser, and a fast-response C&C vessel. Are you getting it? These are not three separate designs, this is one ship, and we're calling it the Prometheus.")
Wargame point mechanics are great for setting up even fights between diverse sides, but in the narrative would of Star Trek, if you try to send ten Defiants to survey a planet when the mission profile calls for a Galaxy, it doesn't matter if their credit-value is the same, they still can't do the job.
For that matter, there are also resource costs to making it possible for the Intrepid to land and take off, but Starfleet still did it, even though the Cardassians could theoretically build a bunch of space-only Intrepid-equivalent ships that would consistently kick their asses by a nose in an even fight.