Trying to get a better understanding of dependencies and how to maintain the "perfect" system

As a new Linux user, I'm trying to understand how dependencies work so I can keep my system efficient (no or few redundant files resulting from dependency management). I have some questions:

1. 
   

   I'm concerned with leaving behind any sort of files after removing a package. If I have 10,000,000 files in my system before I install a package, I want 10,000,000 files after I remove a package. I read that even after apt-get purge and apt-get autoremove, often times system config files (which the only way I can remove is to manually look around for them, right?) that reside in Home are left behind. More information here: http://ift.tt/1m5VOeQ

   
   


2. 
   

   Removing a dependency will delete the package that depends on the dependency. Removing a the package leaves behind its dependencies (orphan packages), right? Isn't that what autoremove is for? I'm confused as to why a user said it removes the the dependencies as well: "When a package is removed, the package manager lists for removal all orphaned packages at all levels of the dependency chain [1]. If package Z depends on two packages (X, Y) and each of these depends on two other packages (x1, x2, y1, y2), then the removal of Z will orphan six packages: The two dependencies of Z (level 1) plus the four dependencies of them (level 2)." - Source: http://ift.tt/1aeLMVB

   
   


3. 
   

   What's the deal with metapackages and removing default applications that also want to remove its metapackages? I read stories where people want to uninstall an application and apt-get wants gnome-desktop or something huge to be removed as well. Some say its fine to remove the metapackage as its just a container for actual packages that are technically dependencies of the metapackage. Others say there are dangerous implications of doing this. What are the proper steps to take in this scenario?

   
   


4. 
   

   How to maintain dependency chains? In the second link, the last comment (last paragraph) described how important it is to only mark the highest-level of the dependency chain. Why and what are the implications of not doing so? An example: Uninstalling Ktorrent from Kubuntu-desktop leaves behind the dependencies of Ktorrent even after apt-get autoremove because its dependencies were also marked manual by the developers that created the kubuntu-desktop metapackage.

   
   

I appreciate all responses--I have posted similar questions on other forums but do not have satisfactory answers.