Possible different micro ops for different semantics.
They also don’t mix instructions sets within the same process - the diagram I saw had ARM Linux as a guest under z/VM or KVM. For generations now no OS (not VM, not z/OS) hasn’t seen the bare metal machine, only ran under the PR/SM hypervisor, which is what does the logical partitions now.
In order to properly run OSs for the 360 and 370 generations, s390x also has instructions for setting up CPU flags to more precisely emulate older machines. From an s390x binary you can, IIRC, do a jump to an address telling it that, from the jump forward the ISA is the one of a 360 until it encounters a return, which restores 390 mode.
I found this article with the diagram that you mention: https://wccftech.com/ibm-worlds-first-dual-architecture-proc...
The diagram is the last picture, and according to it you choose the ISA at the VM level: either Linux on s390x or Linux on arm64, but not both on the same VM.