Best practice to track custom software installations on Linux in /usr?

Have you tried checkinstall (it's in the Debian repos)?

Instead of using make install you can use checkinstall and it will create (and install) a package with the software so that you can track it using your package manager.

Since you asked for best practices: The best one is to don't install software not in the repositories. If that's not possible, the best practice is to build packages out of it and use the systems package manager to manage them.

You will need to come up with a way to check for important updates, but how you do that is up to you. But if they are there, you need to build again and update from the new packages.

I dunno whether you'll find this helpful at last, but I'll share it at least: «… The NetBSD Packages Collection (pkgsrc) is a framework for building third-party software on NetBSD and other UNIX-like systems …»