My understanding is that branch prediction got better in the ‘10s and a bunch of techniques that didn’t work before do now.
So, while it's true that microarches changed in a lot of ways, the overall implications for how you build VMs are not so big.
It's true that predictors are able to see through multiple levels, but a threaded interpreter gives them plus one level, and that ends up mattering as much as it always did.
They got better than they had any right to be, but then we found out that Spectre & Meltdown were vulnerabilities rather than optimizations.
For example, a switch based interpreter was fast as a CGOTO one for a brief period between 2012 and 2018, but suddenly got slower again as the CPUs could no longer rely on branch prediction to do prefetching.