It's unfortunate how some people will assume anyone whose opinion is different from theirs must be posting out of ignorance and not experience. If someone is critical of Linux and posts in a discussion where Windows is also relevant, you don't have to jump to the conclusion that they need to learn what chroot is or don't realise that su'ing to root on Linux is not directly analogous to allowing administrator access on Windows.
Let's consider a real world example I dealt with not so long ago, maintaining a system that is used for multimedia work. In such systems, FFMPEG is a commonly used component. You probably want some audio and video codecs to go with it. Those in turn might depend on various tools to build optimized code. And if you're running on a stable distro like Debian as your foundation, the distro-packaged versions of all of these tools will be old, so you almost certainly want to fetch and build recent versions manually instead.
Before we continue and I tell you what the actual maintenance problem I had to fix was, please tell me how you would set this up. That way we can easily see whether your "many, many ways to handle this" that I (or presumably, in this case, the guys who first installed the software) might "care to learn" would have worked out any better than what was actually done, and at least one of us will learn something.