I wouldn't say that Kid's involvement is absolutely necessary for the DC manga. Other than that one scene on the Mystery Train, I treated it like a side-plot because his involvement has never resulted in and is not necessary for plot progression.
Just because it's possible that Kid may be facing BO members doesn't mean it's true. And I wouldn't go as far to say that it's "probable" either.
The BO is a more realistic take of the MK Organization because the hunt for Pandora (a gem that supposedly grants immortality) is simply too unrealistic of a plot to be a part of DC--it ruins the realism that DC was originally established on.