Be....cause the tonnage for a 100 Kton Warship's maneuver drive and a 100 Kton Dropship's maneuver drive are not the same?
Physics doesn't particularly care as long as it provides the appropriate amount of thrust.
That's really the problem with trying to compare them using real world aircraft engines and the like. It's a completely different environment with much simpler requirements for getting the thing moving. There shouldn't be any particularly good reason why a physically impossible fusion torch able to push a hundred thousand tons of spacecraft at one gravity of acceleration in space couldn't do the same to another hundred thousand ton spacecraft arranged in a different configuration. "Because they're not the same" isn't much of an argument.
I mean, heck, if we're going by what the rules say, the behemoth drive might be even harder to build than the warship drive, since the dropship engine is more fuel efficient (8.83 tons per burn day vs 19.75 in strategic mode) and the rules presume a dropship is able to operate in an atmosphere. All dropships use the same engine equation and the Behemoth's thrust only prohibits it from landing in standard gravity, and the specific prohibition against atmospheric operations is an optional design quirk, not an automatic rule.
Now I'm not saying warships should get dropship engines. The design rules are broken enough as it is. But from a purely fluff standpoint, there's no reasonable reason a behemoth's transit drive couldn't serve as a decent starting point for developing a slightly simpler transit drive for a similarly sized warships. "It doesn't work because reasons" isn't much of an argument.
Truth is, the writers wanted to create a limitation and didn't think too hard about it. A better option might have been having problems producing a structurally stable design of that size able to handle such high acceleration (Dropships and Jumpships tells us the Behemoth is prone to structural problems above one G of acceleration due to its great size, a nice starting point), possibly magnified by the need to keep a long, thin germanium core intact, requiring engineering assistance from Comstar/the Word of Blake.
However, "they needed transit drives from comstar" is the reason we got, so we're stuck with it. With that in mind, I'd probably go with saying the behemoth drive didn't provide the power they wanted for the hulls they wanted to build, and they were too much of a hurry to put the work into developing a bigger drive. They needed to close the
warship gap.
Sure, a hundred thousand ton vessel tooling around with a behemoth drive might have gotten a ship in the field faster, but nations don't just build things based on pure logic (in fact, pure logic is historically in critically short supply). They've gotta sell their leaders (most of whom have no naval background whatsoever but who decide where the money goes) and their public (most of whom have even less) the
idea of the ship. That this is something that will protect their people from another Turtle Bay, or Turtle Bay the hell out of their enemies, and that the compromises they make are worth when these ships might find themselves running up against ships many, many, many times their size (if not necessarily their raw capabilities).
Hell, I still remember Davion
fans complaining about how House Davion was stuck with a bunch of Foxes for a lot of their fleet, even though the Fox is arguable the most sensible "starter design" out of all of the Inner Sphere's warships. Imagine that, but they're the nobility who holds the purse strings or think they can lobby your perceived "foolish endeavors" into additional political power.