Exactly how natural or frequent is this word order in hebrew? In english it is somewhat Yoda, at least to my ears
Depends on your point of view. Your sentence describes the same world, but has not the same construction as the hebrew.
But translations don't require to keep the original construction. It may even sound awkward in the target language. In this case I don't see why it was not accepted.
I absolutely agree with you in the normal conversation. When learning and practicing, however, I think it is good too to work on exactness. It's easier to relax in daily use.
Do you know why it's "in" the glass vs inside the glass? For instance, what's in the glass? Would you use bet - in, or betoch - inside? Is there a rule about liquids or something similar when to use which?
Could you say: הכוס, יש במים? If so, would it sound different than the example for this skill because instead of בה מים, I heard, במים. (What if you wanted to say, there's a glass in the water? Like if you dropped a cup in the bath. Thanks).