As you probably are aware, an apparent workaround for this apparent bug is to make a toplevel "container" system, whose only contents is a :depends-on which contains the actual desired system (or list of systems). It seems that if the toplevel system has no actual file components, then it will not appear in the (asdf:component-depends-on 'asdf/bundle:monllithic-fasl-op ...) at all, and subsequently the systems appear in the correct order --- so the generated monofasl will be usable.
In fact that's why I didn't see the bug initially, because gendl.asd normally is just such a container system and has no source components (last night I purposely "broke" it for testing by inclusion of a "source/try.lisp" at the toplevel -- if you clone the repository now, that source directory will not be there, and the monofasl for :gendl will work).
I hope this is useful information.