I don't think you have to have systems in the same thread/process if you have bake in an API for controlling time and ingress/egress for each component. (depending on what you're trying to test) You can have the communication channels between components under the control of the simulation environment rather than have them happen in their 'normal' manner. This allows you to inject latency between components, 'fiddle'…
The reason for using a single underlying thread/process is to prevent the OS scheduler from interfering with deterministic execution. You can't control how and when the OS scheduler kicks in, nor can you perfectly reproduce the clock drift/jitter between multiple cores. If the program under test spawns threads, then you'll have to emulate the execution of those threads by writing your own scheduler whose time slicing…
Also, scheduling is independent of deterministic execution unless you are doing inherently non-deterministic things like multithreaded shared memory accesses which you can not simulate faithfully anyways. The only thing that matters in a deterministic execution model is runs of deterministic execution interrupted with non-deterministic events injected at precise points in the execution trace.
When serializing onto a single thread you already need to define some sort of correspondence between "simulated scheduler state" to number of instructions to execute as you are already giving up on the actual scheduler (unless you do not care about correspondence to the actual schedule configuration). You just do that, but you get to execute with all of your cores until you reach the injection point (which is how replay systems can work already). Now you can execute in parallel (multiprocessing only though, no multithreading) and use blocking I/O.