PMDs are perfectly safe to read from.  Have external binaries On is a matter of debate. Some people say they still have issues when PMDs are used to write scenes and saving to the library, others do not have these issues. I have used it for the past 2 years and I have no issues whatsoever.

What advantages do external binaries offer?
It uses less disk space. The morphsets are written to a PMD in a binary form and are re-used. It is also a LOT faster in saving and loading scenes and figures. And as you said, there are advantages to be able to create morphs in figures outside of the INJ system

Disadvantages?
As I said above - some people consider external binaries unsafe.
Another is that PMD files are not directly usable in DS

Regarding memory usage - I don't think there is a difference. It could be that morphs are loaded on the fly, but I am not sure about that.

Hope this helps