This is all true and that is why its so important to practice apps with a partner...but, as far as "reverse engineering" forms, that's not necessarily a bad thing. I always liked it when a teacher asked a student what do you think that application is. If they come up with something practical then train it and make it work. It gets them to think for themselves on how to apply the art.
We all know there can be several applications for any given move in a form..some may work better for you than others...Certainly a lot of apps are hidden and need to be explained, but a lot of stuff can be discerned just by looking at it and two people can come up with two different apps as their first choice. The apps you recognizance on your own may work naturally for you.