That's the problem - you have two completely different installation methods, neither one of which is particularly UNIX-y, and neither of which is capable of talking to the other in a reliable manner.

> IMO is better than the usual package manager in a linux distro

It's incapable of handling binary installations, which is remarkable considering the hardware variation is far less than there is for Linux, it installs to /usr/local, it doesn't integrate well with language-specific package management tools, and it can't update system files.

> it doesn't litter the disk with init scripts or config files

I've never once had this problem with Linux; the man pages for any Linux package manager should provide a straightforward way of figuring out which package own which files.

> you always know where things are being installed to.

Because they're not installed to the right place.

I can't count the number of times an OS X package has told me that I need to add such-and-such folder to my $PATH. Hint: if you're requiring me to change my $PATH so that your installed file works, you're not installing it properly.