It does not seem like netgen merges devices that are comprised of both parallel and series fingers. Is this desirable behavior? Should I never be doing that? Is there some option to enable it?

Just bear in mind that netgen's goal is to match things, not to merge them. So it will only merge if it can't find any other way to match up the two netlists. Merge behavior is pretty well described by the setup file, although there are a few obscure ways to make the matching fail.