This is less of an issue with JS, but say you're developing this C++ application. It relies on several dynamically linked libraries. So to run it, you need to install all of these libraries and make sure the versions are compatible and don't cause weird issues that didn't happen with the versions on the dev's machine. These libraries aren't available in your distro's package manager (only as RPM) so you will have to clone them from git and install all of them manually. This quickly turns into hassle, and it's much easier to just prepare one image and ship it, knowing the entire enviroment is the same as when it was tested.

However, the primary reason I use it is because I want to isolate software from the host system. It prevents clutter and allows me to just put all the data in designated structured folders. It also isolates the services when they get infected with malware.