Is this kind of on par with the German "doch" or the French "si" as a "yeah huh!" response to a negatively-worded question? Example: "You're not Aunt Toma, are you?" To which a "no" would be a "nope" response but a German "doch" or French "si" would be like saying, "actually, indeed I am."
Is that what this "It is so" means, or does it mean more of a "so it is written, so it shall be done!" kind of statement (NOT in response to a question)?
No, it just means "it is so"... You want to find some context? It is just an agreement with a statement, not even necessarily an answer to a question, for example, Тітка Тома там - Це так (Aunt Toma is there - Yes, it is so)
Although I actually don't say it this way in real life, to be honest :)