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日本の会社が初めて作った口から飲む薬です。
It's a medicine which you take by mouth that's made for the first time by a Japanese company.
I was surprised to see 口から here. I can only guess that this is from the perspective of the inside of the body. Q: "How did it get in the body?" A: "It came from the mouth. " Is this the correct way to look at it?
If I'd written this sentence myself I would have use 口で meaning "taken by means of mouth". Would this also be grammatically correct/natural?
口で飲む would be comically redundant because the act of 飲む always involves the mouth. 口から飲む is redundant for the same reason. 日本の会社が初めて作った飲む薬です is just fine. 口から adds emphasis on the fact that the drug is administered "from the mouth" as opposed to other possible means. The mouth is seen as an entry point into the body.
から expresses the starting point. In your case: the mouth. Because the medicine goes in coming from the mouth. You're not taking intravenous injections, for example.
Using 口で seems fine, but the emphasis becomes the way you do it and not the spacial position.
