Not a reason that most people accept, but yes, there was a reason. Several, even.
In essence, they made the bottles behave like all other items that have containers; IE, Gasoline, you never have to have a gas can, you just get a gas item that has a gas can icon, and when you consume the gas you dont get a gas can, it just goes away again. Similarly, the bowls and plates that appear in meal icons, or the way you dont get brass shells back after firing your weapons, etc. Or how you dont get candy boxes from the candy items, or cans from the canned food (empty cans were a thing but were removed for a similar reason actually)
The containers for items are just a nebulous thing that represents the item.
Another reason they were removed is that having access to a refillable bottle, even one let alone being able to craft more with ease, made water survival a complete non-issue- You take your one bottle to a water source, fill it, throw it in the fire, drin...
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