It would be nice to see some official "direction" about what the more careful derivative vendors that choose to implement the new hardware are SUPPOSED to do
@westfw, you hit the nail on the head. I think once that happens, worries like those expressed by the OP will go away. Until then there will be people worrying that this is some form of lock-in technique.
I'm sure the Arduino team have been busting themselves getting all this ready technically though, and things like publishing a hypothetical "VID/PID allocation policy" have been way down their priority list if it's even on there at all.
So far people have been saying "it's a problem", but nobody has actually said what they'd like the solution to look like. So here's my take on it.
Ideally, I'd like (as a third-party board manufacturer) to be able to apply to the Arduino team for a PID issued under their Vendor ID. I'd be quite happy to pay some appropriate fee for that privilege. I'd then like a published list of assigned PIDs and the boards they have been assigned to, making it clear which ones are official Arduino products and which are not.
That could end up as an administrative nightmare for the Arduino team though, and I can see why they'd probably prefer to avoid the whole issue and just tell third-party board developers to do it themselves (ie: pay the US$2k fee for their own VID and get on with it). It would also be tricky making it equitable: would it be a flat fee for a PID (which would favor third parties who manufacture in high volume) or would it be a per-board-manufactured fee, which would favor people who want to build only a couple of something for their own use?
It's a more complicated problem than it first appears, and my opinion is that the Arduino team will probably leave it up to other developers to solve their own VID/PID problems rather than do it for them.
A simple official statement along the lines of "we will not be issuing PIDs to unofficial boards, and the Arduino VID is reserved for official use" would clear this up once and for all. It's not the ideal outcome I'd like, but we'd know where we stand.