Armor: It's a station. It ought to be able to take a bit of a beating.
MEGAMI: It's possibly going to handle interfacing with many other -IES units. I'd wager a yes, if only for that. The Ayame-class does the same thing.
Fitting in a Plumeria: Well, it should be able to fit in any ship we consider a non-capital ship - at least one inside - to be able to build one (not that the station would be actually intended to build starships, but it would have the facilities to do so if it really became necessary. Otherwise, it'd just be like a very effective central dock).
The small station I had in mind had an upper section with the control/communication equipment, power systems and the living areas. Then, there was a central section which actually was a construction dock good enough to build a non-capital starship. The outside of the central station had three deployable drydock frames to service ships not requiring the facilities of the central section (minor repairs, maintenance, refueling, rearming). A docking ring with several arms to dock ships on would have room to support ships on standby and then a long stem designed to attach cargo containers (is the manner of DOCs, which the Odori's more around) would hold the supplies of the station.
All in all, a spindly but rather servicable facility. The Ikoi might not match my ideal picture, but it does come a lot closer to it than the huge star fortresses from before could.