Why are there two sets of tools and bootloaders in the Arduino IDE?
Arduino IDE comes with a "platform" (the arduino AVR) in the Arduino\hardware folder.
Then you can add/upgrade platforms with the boards manager.
These will be installed in C:\Users\\AppData\Local\Arduino15\packages.
The reason for this is that Arduino IDE wants to be able to "work out of the box".
If they did not deliver the platform inside the installation/zip a "installation finishing" job needs to run after opening the Arduino IDE.