"Are you aware" always seems condescending to me. It's a weird assumption to make that because someone made a choice, that they weren't aware that there were other choices.
It's like walking up to someone who drives a Honda and saying "are you aware you could have bought a Ford?"
Please help me, us there another interpretation of this kind of phrasing?
If you are taking it as condescending, that is on you. It was simply a question.
Tone is an essential, unavoidable, yet undefineable thing. There's a geek fantasy that humans communicate logically and explicitly using only literal meanings of words, but the reality is that most human communication is in body language, tone, emotion, context, and more - and there's no way to define exactly how all those work or what they mean.
I got the same impression as the GP. I'm not always great at it myself but unless I make sure my tone conveys what I want it to convey, I'm rolling the dice.
Phrasing your statement like "my corporate year starts on November 15th; is there any way to offset the start of the year?" would sound nicer. If the author was aware of that and didn't add the feature, then they can say so. Or if they weren't aware, they can say "good idea". Now nobody has to get defensive and the heat of the conversation can generally decrease, keeping everyone happy and polite.
Maybe something like "This looks good. Would be nice to see it extended to support companies that do not follow the calendar year.".
I know this, because I have to self-correct my own communications because of the same or a similar problem (a bit on the autism spectrum).