Yes, AACOMAS only uses the latest grade in a course to figure the GPA, BUT every course is listed on the transcript so it is known that courses were repeated. The other caveat is that the course has to EXACTLY match the course you took before. For example, if you took an algebra and trig course and got a ‘C’ or lower, you cannot replace it with a basic algebra course and a basic trig course. It has to be the identical course; general physics cannot be replaced with physic 1 and 2; etc.
Like Tim said above, though, most people can’t repeat every class. But, if you have some, especially BCPM courses, then it might be worthwhile to repeat them. I think that would be true regardless of whether you are applying DO or MD. The better grades in recent coursework are always a plus!