However, the nature of the replacement VM doesn't really matter in the context of what we're describing here.
The problems of compatibility remain the same regardless of whether the target VM is a JS-specific VM, or a general purpose VM; reliance on undefined behavior, accidental changes in semantics, optimization bugs, and so on.
If browser makers were able to swap-out the VM, they've already demonstrated the ability to solve the exact same kind of compatibility problems they'd face here.