I think Richard is saying that if you implement a subsystem like a to do manager then that subsystem should be all you need, not a bunch of other unrelated parts that happen to ship in one package.
To manage your todo list, you need some kind of format.
There are lots of alternatives.
Org has its own.
Look at org-element.el, the parser for the Org syntax.
Org is built around that.
I don't see Org as a bunch of unrelated parts:
they are very related by the shared syntax and parser.