I think it's 100 dollars because MS has to pay Nvidia royalties based on the backwards compatibility option. If you need the HD for backwards compatibility and MS included it in the core package, then Nvidia would make cash off of every 360 that was sold. MS probably wants to push that cost off as much as it can.
They should just take the financial hit and include the HD in the 299 pack so each unit can have the HD as a standard item. I don't have a HD TV or a Windows Media Center set-up, so I would have no use for the extra items that are included with the 399 pack. If their goal is to not make the consumer buy things they don't need, then they really need rethink what is included in the 399 pack. If I'm not going to use the remote control, HD cables and XBL headset at launch, I'm still wasting money that could be put towards a game or two that I might be interested in trying.
I also don't want to see the HD mainly used as one big memory card. Having the thing included with every system might lead to developers actually making some significant uses for it. The 2 choices idea might cause third parties to code games as if the HD does not even exist, and that would be a waste of something good.
It was important to have the HD as a standard part of the original Xbox and now MS is might nickel and dime the 360 out of being more than just an upgrade. I want to try out Gotham 3, but with Sega keeping their in-house 360 games hidden and the whole HD issue, I think I'll hold off getting the system at launch. I'm still interested in what the system can do, but there are some negatives that MS needs to work on.