I'm thinking the continued availability of a bare bones SKU may be dependent upon initial 3rd party support.
Some sources allege something as high as 60-70% of all developers (specifics would make this claim more believable) are currently developing projects for use with Natal. Presumably projects that require the add-on rather than offer optional enhancements.
If the majority of all developers were actively supporting Natal, then it is a much safer bet for MS to include Natal with every SKU as a part of the "base" console. If not... that's a fair amount of cameras that could potentially be sitting in console boxes unused. Kind of like the component cables no one with an HDMI HDTV uses, or the headset if you don't actively chat while gaming, only more expensive.
However, since Natal is supposed to function as an interface for the console GUI, realistically, anyone with an Xbox could use one even if they had no interest in the current games being developed for use with the peripheral.
The important thing to consider, bundle or no (specifically for the entry level SKU) is the price. If they have to increase the price of the base SKU, then I think they'll still have to offer a bare Arcade SKU or risk losing the entry level game consumer who won't pay more than $200 for a game console.
But since the Arcade SKU does not make up the majority of Xbox sales, I don't think this would have much, if any effect on a developer's decision to immediately support the peripheral with a Natal specific title (supposedly, most are already doing this anyway).
And if MS can minimize losses through manufacturing price reductions on the console itself and still include Natal kits with current SKUs at the same price, all the better. Everyone wins. 100% adoption for new Xbox owners, no extra cost for the consumer, developers have the assurance that all new consumers at minimum will be able to buy and play their Natal specific games.
If MS really wanted to be kooky, they could potentially charge enough for separate Natal kits (say, $149.99) that existing consumers would simply find more value in buying another bundled console intead (assuming that $199 Natal bundle many are banking on happens).
Personally, I think the bare Natal kit will still cost well under $100, unless the above is MS' strategy.
If Natal was over $100, and a Natal/Arcade bundle was $199, I would imagine quite a few existing owners would simply buy another console.