Steve,
I think the solution is the Checkout process, i.e. select color and size options at checkout time. That might make Auctiva checkout a logical place to implement the change (and perhaps eBay with its other properties is thinking likewise to move more and more to full Retail model).
Tieing that to inventory and always showing correct onhand inventory in the listing is then a must and/or backordered with date available. The only thing that makes me nervous on backorder is buyer negs for not reading what's written (that's another subject for discussion).
In the mean time, one color on the Floor (auction or BIN) and the rest in the Store to keep the order straight is probably workable. I'd show all my colors and size options in the auction listing and point them to the Store, where listing is cheap. Folks have often done that anyway, but I think this policy suggests it's now sanctioned from the mountain top.....with more Commandments to come.
I posted the FULL policy release in the eBay Talk section of the Forum.
Danno