I have always wondered why this is the case as surely an app could be made that does this? automates the manual deletion? or make an app you install other apps via that keeps track what folder/files are created so it will know what to delete if removed?
Does deleting apps from the MAS get rid of everything? or is ot the same as pre app store?
Yes, it could be done to a degree. You would have to put restrictions around what you will touch.
I have an Alfred extension I wrote that handles some of this, but it is artificially restricted, instead of searching for files with some name related to the App, I do the following:
Grab the CFBundleIdentifier from that App's Info.plist. This gives me the name a good developer would use to reference files associated with that app (reverse domain, for example com.panic.Transmit).
Using that, I run through and delete Preferences, Caches using that CFBundleIdentifier and lastly the app itself.
There are issues with this method: Bad Developers who do not use the CFBundleIdentifier for identifying their support files. Google Chrome or 1Password for example, do not do this for caches.
For Chrome caches, you would need to go into ~/Library/Caches/Google/Chrome
Of course, Preferences and caches are a small piece, you have receipts, frameworks and many other files. Maybe you tried two apps from the same developer, and want to delete one fully but they share a common Framework. There isn't a really good way to determine such a case, and you end up with bad results.
In short, there isn't really a good way to handle this stuff in a way that gets everything and has no chance of being destructive.