How do you render complex polymodels with mixed textures in a single render buffer batch? Afaik that's not possible (unless you put all the model's details in one texture and access them via texture coordinates). Still you shouldn't just render transparent (alpha blended) faces in a single batch that are far away from each other, probably with other transparent stuff between them. At least not with the techniques I know of.
when the models are loaded a vertex buffer is made, and a different index buffer for each texture is made, when the models are rendered it goes through each texture and draws the related index buffer (obviously using the buffers related to the current LOD and skipping empty buffers). objects are sorted back to front. transparency was never intended in the design of the graphics system, but alpha blending was enabled so some effects could be performed (cockpit glass) if the modder was willing to jump through the hoops to get it working. the assumption when drawing transparent stuff on ships is that there is not a lot of stuff between the transparent poly and the opaque surface behind it (oh, another assumption, there is an opaque surface behind all transparent textures on ships). These assumptions work well enough for 90% of the transparency effects people want in FSO, though some effects don't fair as well as others (any time you can see a transparent surface through another (like big bulky glass domes) you get problems).
freespace's geometry is all stored in BSPs so you can sort it very efficiently if you need to. this is something that has been tossed around from time to time, usually as part of the elusive materials system.