How would it be possible, without changing anything about 2009-2016 year model cars that the Non-B part fit, for the B part number to not work with them? Or vice versa? The fitment page I listed from VW shows the B part is compatible with older applications, so it is definitely "backwards compatible" at least.
The Helix DSP has no link or data interaction with the car to check the year or model of the vehicle. It just takes the speaker level outputs, applies DSP settings based on what the user programs, and reamplifies that signal. There is nothing to how it functions that would not allow it to work with any vehicle with the correct connectors in the dash and an appropriate program through the dongle. Even without programming, it would still function but sound would not be optimized.
I've said it before regarding the B revision, this is a new production part and may have some very minor changes from the Non-B part. For all the research I've done, any changes would have to be internal to the DSP or sub box itself, as visually and functionally they work exactly the same. Even the same programming dongle works on both Non-B and B kits. I don't see any reason to treat the new B part number as anything but a revision part number.
Manufacturers will have revisions on parts to denote a change and track sales, warranty claims, etc. Helix/VW added a B to the old part number for this revision. That way if they start having large numbers of failures on the B part for example, they can be returned or recalled, or at least identified. Then they would resolve the issue and release a "C" part, etc.
The reason for the close out was likely because the inventory of the B part number was ready to ship to the US and in anticipation VW closed out the old stock. It's not a great idea to have new and old product mixed it a warehouse, so you use that clearance to make space for the new incoming product.