Where does Android store the binaries of the apps themselves? In operating systems like windows there is a special folder like Program Files where the executables themselves are stored. But in android it's kind of amazing that the binaries themselves are hidden after their installation via an APK file, and the APK can be deleted safely. Moreover, the only way to uninstall an app is via the application manager! Can anyone give me insights to the reason behind this design ?
Just answering as the comments suggested,

 /data/app/package.name/base.apk


The APK File is placed inside the data partition.

This is different from Windows as you mentioned.

Windows uses a different protection for System Software called UAC (User Access Control)
whereas Android uses a separated Partition on the HDD ( SSD ) called the System Partition.

All Stock Software is stored under 

system/app/*app name*/app name.apk


&amp;

system/priv-app/*app name*/app name.apk


or

system/app/appname.apk


&amp;

system/priv-app/appname.apk


Additional Software from OEM's is usually stored under

system/vendor/app/


However since the new partitions in Android 7.0+ i believe that Vendor is now designated its own partition, making the app directory

vendor/app


Or similar.

Some Vendors put APK's into the system tp be automata installed also under "custom" partition or root folder

custom/app


Furthermore, applications can be built by binaries under 

system/bin/


&amp;

system/xbin/


If you're the Administrator of your PC, you can hypothetically destroy the systems integrity on Windows - however due to any changes being placed in /data partition on Android, you can not delete system software or destroy the system integrity without root access.

The data partition &amp; cache partition hold every single modification made to the device - this means a "Factory Reset" just Erases the Data &amp; Cache partitions on Android - VS windows reinstalling the entire system from a separate backup partition.