You are explaining potential implementation methods, but I think implementation method is a secondary consideration. The more interesting question is what is the simpler and more likely explanation. I think envisoning thought as a sprawling system (through space/time), creating temporary localized identities, through clustering & evolving preferences is simpler than the one with non-mutating preferences. It is non-dualistic, doesn't require multiple layers, etc.
> That substance, though having a changing state, is governed by immutable (as we notice so far) laws of physics
You are mixing layers - substance & laws it seems to be governed by (law is a "meta" substance if you will, or properties derived from a given set of observations). To create immutability out of mutability, you need to build sophisticated layers... That makes it a more complex explanation (and less likely explanation).
Moreover, having a mutable/evolving identity doesn't preclude it from being governed by immutable laws.
Just a matter of applying occam's razor.