Are chaplains expected to know the basic tenents of all these obscure denominations?
No, but they are expected to respect that "obscure denominations" have their own beliefs, to know where to go to find out about particulars, and how to accommodate such beliefs.
Part of the establishment of these faith groups involved making those pieces of information accessible resources.
Your question strikes me as "is an IT support specialist supposed to understand (insert comprehensive list of programs supported by the IT office here)?" When the whole point of the list itself is to act as a search index for finding that information on the fly. It is not "individual knowledge" but "organizational knowledge", and that "organizational knowledge" is being fucking deleted.
By deleting most of the list, now the chaplains will find themselves unable to find those resources, and the lack of official resources will be used to leverage non-supportive actions: "yours is not a recognized faith, and as such I have no obligation to respect it" is a sentiment perhaps not often spoken in the military out loud, but which I have nonetheless heard said between the words.