Aluminum bottles/cans are lined with plastic, to prevent the liquids acquiring a metallic taste. Beer cans are usually lined with BPA - which is bad news for your endocrine system. Sigg bottles have recently moved to a BPA-free lining, but it's still plastic.

I think their concern is others’ disposal of the glass on trails.

Edit: though I do dislike the idea of biking with glass bottles, especially in a backpack. A plastic container absorbs impact and can make falls safer. Not so much for a glass container.