After submitting I went back and rereading my comment and realized that you were responding to my response to phoddie's description of VMs as perverse sledgehammers.
You are correct that my previous comment is not correct with respect to how Nix operates. My point (poorly expressed) was that a package manager is either going to introduced a combinatorial explosion of potential conflicts or be VM-lite by supporting independent package installations.
I'm objecting to the suggestion that VMs are a perverse sledgehammer. I think they are a very good sledgehammer to quickly roll out lots of independently configured instances. If Nix+Containers can accomplish that while eliminating some duplication then VM-lite may be preferable to pure VM, but that has nothing to do with user-installed packages.