Obviously, if a necessary feature is available only via tar-ball, then that is the only possible solution.
Lets rephrase: Avoid
unmanaged installs.
What does that apt-get & kin bring to the table?
http://en.wikipedia.org/wiki/Advanced_Packaging_Tool
Software management
That manager doesn't know anything about your unmanaged installs.
You state that building self configures to your system. Can you be sure that the package management doesn't?
You state that repositories of your distro lack latest versions. Sounds like you don't use a distro that focuses on being the bleeding edge.
You state that packages are not compatible. If this is within single repository, then the repository has serious maintenance issues. If it is due to multitude of third-party repositories that formally package for same distro, but overlap and differ in ideologies, then you have to choose, rather than take everything. How do you find out the incompatibilities anyway? How do you know that your unmanaged install doesn't conflict with something?
Easy? Managed install downloads the package, solves dependencies, and can update those packages for which there are updates. Critical security updates can be on separate channel, so that you know to get at least them.
Sure, you do type about the same amount initially. However, it is easy to type
rm -fr / too; it is the followup where the managed system shines. Package manager knows whether the repository has updates. How much effort do you spend on checking that each unmanaged application stays up to date? Why would any distro have package managers and repositories, if unmanaged source installs are so easy and preferable?
Not all tar-balls use GNU autotools. Hence, same routine doesn't apply to every case.
What if your system lacks some library? The configure can either abort with more or less useful message or skip building some parts of the application. The OP would have hard time in both cases.