It doesn't make a lot of sense, the original GAC was already quite capable of storing different versions of assemblies. And there's little reason to assume a program will ever accidentally reference the wrong assembly, all the .NET 4 assemblies got the [AssemblyVersion] bumped up to 4.0.0.0. The new in-process side-by-side feature should not change this.
My guess: there were already too many .NET projects out there that broke the "never reference anything in the GAC directly" rule. I've seen it done on this site several times.
Only one way to avoid breaking those projects: move the GAC. Back-compat is sacred at Microsoft.