EDIT: I should have read your link first. It appears that your system allows for greater isolation and the ability to relocate different versions.
The "boxes" (directories with packages) created with bpt are relocatable, so it is possible to prepare a box with all the applications and their dependencies and deploy it without needing root privileges.
It has first class support for python packages (through PIP) and "autobuild", which is similar to checkinstall. I couldn't find these features anywhere else.
No, it doesn't. I've used stow heaps of times in my home directories on various university machines. The common case is for managing /usr/local, but you can ./configure --prefix=$HOME && make && make install prefix=$HOME/stow/foo-3.14 && cd $HOME/stow && stow foo-3.14 without trouble.
Some months ago I have written a small tool that automates installing apps in separate directories and then symlink them to a directory in the path. It also supports disabling/reenabling/removing single packages (by removing the symlinks) and has a PIP fork to simplify installation of Python packages (also an "autobuild" for standard configure/make build systems)
It was written for development but actually it became my preferred system to install packages in Mac OSX, packaging systems (fink, macports...) are terrible there.
It's on pypi and doesn't require any installation, if you want to give it a try: http://pypi.python.org/pypi/bpt/