It doesn't quite answer your question but I was very interested to read Jim Hugunin's message about leaving Microsoft a while ago.
One of the things that he pointed out was that the DLR was the driver behind many of the nice advances we have in .Net 4.0 that you now say are the reason why you might not need the DLR anymore.
Edit: Link to the messsage - http://hugunin.net/microsoft_farewell.html
On the other hand, I think that the DynamicSite system is still something that's quite valuable to have, whilst not necessarily something important to put in the CLR itself.
2nd edit: this is an interesting query really, I've just been looking at the docs on Codeplex. As you state and clarified, the .net 4.0 CLR does implement the kind of things that used to make the DLR special; Reading the DLR overview, I think that basically the idea is that things that are implemented with the DLR have the advantage of getting access to new features more quickly then waiting for a new version of the Framework.
This might be moot as they've not released a new version of the DLR for a while now!
Another possible advantage, but I admit I've not explored this properly, is that the AST in the DLR has more features:
Shared AST (Expression Trees) -- This is one of the core pillars of
the DLR. We have extended LINQ Expression Trees to include control
flow, assignment, etc. We also ship the sources for all of Expression
Trees v1 and v2 (the new stuff for the DLR). Expression Tres are part
of lowering the bar for porting languages to .NET, and we use them in
the binders and DynamicMetaObject protocols.