Home Assistant ships its own management logic for the dependencies. This works pretty well and keep the dependency tree minimal. Usually it doesn’t make sense to install the binding for X if you don’t use X. The issue here is that there are modules which requires compiling c extensions and this is time-consuming.
The idea is now to use as many dependencies as possible through the distribution’s package management system. Especially netifaces or the whole Z-Wave stuff. This way the installation is faster and the modules are system-wide available.