Modern aircraft are a poor example, because what's listed for their carrying capacity is always a "theoretical" capacity. I've been on many, and the way to get the maximum capacity is to 1) pack people in like sardines, and 2) not travel very far. Distance/payload tables don't exist for BattleTech, because everything is always assumed to be at maximum capacity. A Warhammer which loses both its arms is still treated like a 70-ton 'mech, even though it's lost more than twenty tons of mass and thus its 280-rated engine should move it 5/8 (or even 6/9, depending on how much armor its lost elsewhere).
Now, passenger bays. Since a single Marine gets 5 tons of living space, it's to be expected that the life support systems for that single Marine are far more efficient than an 28-man foot infantry bay, which also masses 5 tons. Honestly, that infantry bay is a steal; 28 times the personnel capacity while only paying five times the life support cost. The difference is that that single Marine can live in the 5-ton bay for long periods of time, and, at least for the fluff, people should get really tired of that 5-ton infantry bay. Visit a Navy town right after a ship returns after 6-9 months on deployment and ask the sailors (or Marines, if you live near San Diego or Norfolk) how much they liked their accommodations.
The real reason that C-130s can carry 96 "troops" but only 64 "paratroopers" is because paratroopers have bulkier gear, and unlike regular troops, they require the ability to stand up while the aircraft is moving. Otherwise, Herk passengers are forced to alternate knees, and the crew will walk on this floor of knees to get from the front of the aircraft to the back. Clearly, not the most comfortable of seats for the passengers! (The jump seat in the cockpit, however, has a great view.)
I agree that, rather than making different costs for types of infantry bays, it would make more sense to give, say, a single 50-ton light vehicle bay for each, say, company of mechanized or motorized infantry. However, this would necessarily increase the time it takes to get the infantry off the ship and into the fight, because the personnel and equipment are no longer stored in the same area.