To clarify: According to the way I was taught to understand Agadata, the meaning is the conceptual meaning. They may be meant physically as well, but I was taught that the physical meaning is generally NOT the (main) point that the Midrash is trying to get across. Yes, of course we have to know what the Mefarshim on the Medrash say and we can not decide for ourselves which Medrashim are meant literally and which are not. And we have to make sure that we do not find ourselves in a position that we can not, chas v’shalom, accept the possibility of a Midrash’s literal interpretation, especially in those cases in which the Mefarshim do say that it is meant literally.
However, my point was that the conceptual meaning IS the main meaning that Chazal were trying to get across (even when it also is true in a physical sense). At least, that is how I learned Medrashim and that is my understanding.