There's been a long-standing bug relating to transparency in X-Ray, predating even the Maintenance Branch releases. The useful term to search for is "alpha blending," and there's two things that need to be done to get this supported properly in X-Ray:
1) There's a couple of OpenGL calls to make while rendering those objects; that bit's trivial.
2) Objects which use transparency must then be rendered from furthest-away to nearest (according to the camera position). That's where it gets tricky.
Implementing #2 is far from trivial (or at least, will require a some rather different methods of rendering than we're doing right now.
So anyway, I'd love to get this squared away at some point, though I'm not going to make any promises about timeline.