I've mentioned using a separate partition for /usr/local to install apps, this coupled with a /home part make my systems quite flexible when it comes to OS or application upgrades.
I have yet to see a package manger that installs applications or libraries under /usr/local/ they will usually mix them up under /usr, with libs in /usr/lib and executables under /usr/bin. maybe some apps will go under the /opt directory tree. Odd when you think most application sources you download default to installing under the /usr/local tree.
Package manager are ok for the inexperienced or desktop user. I would image that HD bloat and redundant installationb of libs are just one symptom of packages. I don;t necessarily think Compiling a great thing but it does test dependency functions not just that the name is registered. if these linux distros with the sooper-dooper package mangers can build a decent manager that checks for dependency functionality and allows for custom installation I'd use the fuckin thing. It is a lot easier that configure, make, make install.