You are not alone.

I have external binaries on all the time. I do get sometimes (very rarely) a PMD error but that did not seem to have an effect on any of the morphs which were present in the scene.

SR3 had fixes for issues with external binaries and that seemed to have solved the ones I had in the past for me. One of them had to do with the way you work: Accumulated saves (Save As) under certain conditions would result at one point in a corrupt PMD.

The big advantage in having it on is that speed in saving and loading a scene. A very large scene  will now save in 2-3 seconds which used to take up to a minute without external binaries.