I'm not sure what you mean exactly!? You can't mix transparent and non-transparent polygons in one object...you just can't. If your models contains both, it should be exported in a way that the transparent and opaque parts are actually loaded in into different Object3D instances. Just don't merge these into one in your code and you should be fine. If that's not the case...tough luck.
Then there are models where transparency doesn't really work will (because it's not order independent like opaque and if the object has overlapping parts, it might look strange from some angles). If that's the case, you could revert to stippled alpha instead, but you need your own shader for it. I could provide you with an example if that's needed.