1) It is an indelible mark. Reuse the bottle endlessly, as long it is not broken, and the marking will still be there. Erasing it means breaking it apart and sending it to expensive re-molding procedure. Tampering with a sticker label may do but seems very awkward.
2) It tend to prevent others from reusing the package. The manufacturer owns it, but not anymore when customers pays and landed the hand of related manufacturers. However, the bottle embedded label tells the otherwise. Why use such if you have high pride?
3) A free promotion. Imagine how much free promotion the Ginebra San Miguel is getting by just embedding their name on Ginebra Gin bottle. The bottle is being reuse by producers of soy sauce, patis, cooking oil, vinegar and other non-food items.