Well, modules in styles are added to what is already in place, and identical module earlier in the history are overridden, just like when you add the modules by hand.
Now, the dilemma is what to do with automatically added modules with auto-selected values: in some cases, you want to keep the auto values, in others you want to override the automatic values (e.g. because they are wrong for certain cases, or you don’t like the automatic values)…
Also, IMO styles should contain the minimum number of modules needed to get the effect you want. Reason: if there are extraneous modules, applying multiple styles can have unexpected and unwanted side effects, because they override earlier applied modules.
So, while a warning when you include automatically applied modules in a style could be useful, it’s also a bit patronising, in that you don’t trust the user to know what he wants.