I know it's a nooby question but I really want to know this to stop worrying. I really do appreciate what KDE team offers but I always want the freedom to replace.
I'm using Ubuntu 16.04 (Actually Kubuntu 16.04 on my desktop and Xubuntu 16.04 on my netbook). I've tried to install KDE several times with apt install command. Every time I ended up with an unstable experience and tried Kubuntu, it was flawless. I've learned KDE doesn't mix with especially GNOME and GNOME variants. My question is, let's say I've installed Ubuntu Unity or Ubuntu GNOME, or let's say I wanted to switch from KDE to Unity or GNOME on my desktop computer. I did change desktop enviroment from Unity to GNOME before.

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apt purge unity* lightdm* playmouth-ubuntu* -y && sudo apt autoremove -y && sudo apt install ubuntu-gnome* -y

did the trick. But I want to know if I can use the same method for KDE too. Because I don't wanna end up with messed up configuration files. If it's configurations mess things up I will stay away from this method and basically I will use Kubuntu iso method but can I switch with this method without problems ? I mean like I've made a fresh Kubuntu installation.

For example I come across with such posts on the internet. They recommend to wipe partition and reinstall Kubuntu.
http://askubuntu.com/questions/764542/h ... untu-16-04

There usually is very little, if anything that makes different desktop environments incompatible. I would venture a guess that a significant portion of the Linux-running populace have at least 2-3 different desktop environments installed, be they gnome-shell, unity, lxde, xfce, or KDE's Plasma, and switch between them occasionally without problems.

Plasma can be safely installed along side of any other environments as its configurations are all kept separate so there should be no conflicts.

The differences between the various *ubuntus is primarily in the sets of packages that they install by default, but once installed you can generally install the packages associated with the other environments without problem.

(written from an Ubuntu 14.04 installation having Unity, KDE 4, LXDE, XFCE, Enlightenment, Gnome-shell (which actually isn't working, possibly due to the incompatibilities you mention, but I've never bothered to investigate) and maybe a couple others I can't remember off-hand)

Starting from (K)Ubuntu 16.04, you might investigate installing KDE Neon instead of Kubuntu