First, Does the android system store the "location" of apps when they are on your homescreen/ desktop.
For example, this image has a photo of a homescreen with many apps. In that picture, you will notice apps have locations, IMDB, Gmail, Youtube, are all in their specific locations. Does the android system have a config/ system/ yml file that is accessible and readible somewhere in the system? My intention is to find out the locations of apps, record them, and find a way to re-post them or re-apply them if the icons on the screen were to get removed or taken off. If I can get the pointer/ location of the spot on the home screen where it is located, I can then read that (something like C4, or H2), then I can hopefully reverse engineer how to write the data as well.
The second question is, if the only way this 'magical' file I am looking for can be found is to use a separate Home launcher (Nova, Google Now Launcher, Go Launcher), are there any of them that you recommend asking for help as they are dev friendly?
Does the android system store the "location" of apps when they are on your homescreen/ desktop
No. The app that is the "homescreen/desktop" stores that information. Each home screen can do whatever it wants. It is eminently possible that some share a common heritage (e.g., the home screen from the Android Open Source Project) and therefore may share elements of a common implementation, but others are likely to have been made completely from scratch.
You might consider finding an open source home screen implementation and adding your features to it.