not sure about the specifics of Unity 3D, but in general:
draw solid geometry first;
then draw transparent geometry in back-to-front order.
generally, yes, solid geometry and transparent geometry are kept separate.
in my engine, the chunks with transparent geometry are essentially sorted by their distance from the camera, then transparent geometry is drawn with the furthest chunks drawn first.
this seems to mostly work.
a few things are also drawn with depth-writes disabled, which also has sometimes "interesting" side-effects, but is needed to help reduce problems with intersecting geometry causing ugly self-clipping artifacts. if transparent geometry is drawn in-general this way, rather than out-of-order drawing resulting in things being not-drawn, it will result in blending issues. usually, the blending issues are slightly less ugly though.