Well, to me, PHPCR makes a lot of sense in Products, but I don't see any benefits of using it in the Cart. So the answer is, it depends. Personally, I would be using MongoDB on everything, except perhaps checkout. But I also like the idea of the data mapping in a similar manner to the objects I'm dealing with. However, If I needed some type of versioning with my products, I would go with PHPCR over MongoDB. Early in the project I was a bit pig headed about not wanting to deal with relational dbs, but I have pulled my head out of my ass on that.
Personally, I think those types of decisions depends a lot on what you are doing. My hope is that as people find different persistence layers that work for their particular system, they will contribute those back to the project. In the mean time, while I am refactoring, I am trying to keep things db agnostic. I know for smaller sites, its a lot easier to have a relational db than a document db, so I would love to see both relational dbs and document dbs supported in time.
Richard