I'm nowhere near applying yet, but I think it would depend on whether the classes actually say they were online classes. For example I've taken a ton of online lib arts classes (history, poli sci, lit, etc), but on my transcripts it isn't indicated anywhere that they were online. If, on the other hand, your transcript will be from an online school or shows that they were online classes you *may* be limited in the number of credits that will be counted just like you are for independent study classes. I also imagine some adcoms will have the mistaken notion that online classes are "easy as pie" and look down at them a bit, but since none of yours are BCPM really I don't see why they would hold it against you too much...it's the BCPM ones that they would worry more about I think.
Good luck!