I can't comment on what this guy at Apple did or did not tell you, but if he is a smart Apple guy he should not be implying that any non-traditional setup of a third party product will work. Mainly because he has no product training from Bose to know whether or not it will work. Theoretically it could work, but if Bose does not enable all input ports to work simultaneously, then it's not going to work, and the Apple guy wouldn;t know this unless he read the manual. Just because they may sell some Bose products at the Apple Store does not make him an authority on their use or functionality.
Also, Given what Mchalebk quoted from the Bose user manual, it is definitively clear that it will not allow usage of both inputs simultaneously. If you doubt the correctness of this information then you should talk to Bose, not Apple. I know this ruins your plan, but it is the truth.
As to your comment about the current (old) ATV not having wireless capability like the new one, well this is just not correct. They are both wireless and both capable of streaming from a Mac and accessing the iTunes store over your wireless network.
So, if you absolutely want to be able to listen to music with the TV being off, then you should probably either get an A/V receiver. Of course, in this setup, the receiver would then have to be on while listening to music. I know you are wanting everything to work in harmony together, never having to switch inputs, and everything working in any connection scheme that you can invent, but it's just not reality.
FYI...you can get a good A/V receiver (good brand) for $225-300, and a nice set of bookshelf speakers from $199-299 and still save some compared to the bose system. But if you prefer a simpler setup, then it sounds like you will have to concede having the TV on while listening to music.
Thanks a lot for all your responses and research. This is begining to be a real eye opener!! Now i think i have two options:
1 - use a digital optical splitter
http://compositesplitter.com/digital-optical-splitter
2 - use an A/V Receiver.
(so, with the A/V receiver will I keep needing to change channels to direct the sound then?)
What are the advantages and disadvantages of the two options I have??