Don't most package managers allow you to install to different folders?

RPM:
rpm --prefix=/home/chroot/ bind-chroot*.rpm

or use the --root command-line option to install *.deb to a different folder.

Bearing in mind that most software packages look in "/etc" for configuration - ou would have to symbollicly link the config file.

Also by having everything in one place means that writing scripts to find stuff is easier or physically checking a program "exists" via a script is easier too.

I've used Windows since the very first version and when Microsoft decided to put configuration into a "registry" it means:
(1) you need specfic tools to change entries - with linux a simple text editor will suffice
(2) a single point of failure - its easy to trash the registry and stop many of your installed programs from working properly

I prefer the Linux way of doing things: one central place to install stuff with known standards and each program is responsible for it's own configuration file.

Thats the beauty of it - you are free to choose the method appropriate for you.

You can even slice and dice your Linux partition - your "home" folder can have it's own partition even "usr" - it's up to you.