I was looking at your collection and it occurred to me that an Eagle is essentially a flying HEMTT. If I were in the Eagle business, there would be alien containment, cruise missile launcher, electronic warfare, gunship, LASER, SWACS, tanker, and wrecker pods, For the spine, there would be cargo, crane, fuel, electronic counter-measures, missile rail, and SWACS dome units since the spine essentially functions as a giant ordinance hard-point.
I would also add a cage that attaches to the spine, allowing two, three, or 4 Eagles to connect to one another, spine to spine, and tow very heavy objects. Pods should have a roof hatch that connects to a docking couple, just like the side doors. This would allow people to move from Eagle to Eagle through the roof hatches and a spine mounted, I, Y, or X shaped docking couple.
Come to think of it, given the massive standardization of shipping containers that occurred over the last 40 years, the Eagle should have a pod that slots 4 or 5 such containers, allowing the spacecraft to deliver and load cargo directly from transport trucks. The next step would involve putting standard sized roads on the moon and developing a truck to do the hauling.
On the subject of size, Catacombs has a good article on Eagle size a and related problems. The authors of that article did not account for two additional problems–plumbing for onboard hardware and shielding against cosmic radiation.
For example, the bottom of the passenger pod includes 4 thrusters. In order for those to function. they need to connect by ducts to an engine, much like the ducting system of the Harrier Pegasus engine. That means there must be a couple feet of space between the floor of the set and the bottom of the passenger pod.
Shielding against cosmic radiation is a huge problem for NASA engineers. Without shielding, cosmic radiation will sterilize a human being in weeks, cause cancer not long after, and eventually result in serious brain damage. At the very minimum, all habitable sections require a couple inches of shielding.
The command module needs to fit a powerful RADAR at the very front, just like a modern fighter aircraft. It also needs enough space for life support equipment, landing legs, and a parachute systems since it essentially functions like the escape capsule of an F-111.
Finally, a moon buggy needs to fit through the side door of a passenger pod. There is no other place for it to go.
Given all those requirements, and the economy of scale benefits associated with size, the 102 and 111 foot versions discussed in the linked article work far better than the small alternatives. The cargo area of a C-17 is 88 x 18 x 12.3 feet. A standard shipping container is 40 x 8 x 8 feet. If standard shipping containers slot sideways into a pod we have never seen before, a big Eagle could haul about 5 of them. I have not done my own detailed analysis and cannot advocate for a specific size. I do know the ship needs to be big.