I was responding to somebody who made the claim that installing software leaves things "scattered all over the system". I simply pointed out that that is not true if you plan carefully. Additionally you can ensure that all users on a system have a basic set of paths enabeled in their profile (is the default PATH any more invasive than a default path + "/opt/bin"? These things are not insurmountable if you actually know what you are talking about and know the scope of your problem. These complaints are coming from people who are not actually interested in managing a system, but would rather be able to click a button in a gui and not have to understand anything of what is actually going on.

That being said compiling your own stuff in and of itself is not guaranteed to be a simple or "fun" task. It takes work and can lead to unexpected results: you immediately own anything that is custom on your system and become your own testing, debugging, and troubleshooting team. It isn't ideal.