IMTU, Books 2 and 5 still share.
I switched from Book 2 to HG for every size of ship when HG came out. Whereas Book 2 enforces a small ship universe, HG enable a big ship universe, but is perfectly usable for running a small ship universe.
It's a big ship navy to fight the FFW, but there exist small ship navies to enforce customs, find pirates, and deter interstellar deviance.
That has nothing to do with big and small ship universes.
That the Kinunir is an odd duck in a bureaucracy as large as the IN can call for a colorful backstory, but it should cause for no puzzlement.
I don't know about should or shouldn't, but I do know that it did and does present a puzzle.
Bureaucracies are effective where nothing else can be, but efficiency and rationality in the discrete case are usually happy accidents for them. Worked for at least one my entire adult life...using the term "adult" somewhat loosely.
"I'm sure there must be an explanation" is not an explanation.
Hans