Hardware always involves some level of non-determinism, because the physical world is messier than the virtual software world. Every hardware engineer accepts that and learns how to design solutions despite those constraints. But you're right, non-determinism is not the current problem in
some fabs, because the whole process has been modeled with it in mind, and it's the yield ratio that needs to be deterministic enough to offer a service. Remember the struggles in Intels fabs? Revenue reflects that at fabs.
The software quality at companies like ASML seems to be in a bad shape already, and I remember ex-employees stating that there are some team leads higher up who can at least reason about existing software procedures, their implementation, side effects and their outcomes. Do you think this software is as thoroughly documented as some open source project? The purchase costs for those machines are in the mid-3-digit million range (operating costs excluded) and are expected to run 24/7 to be somewhat worthwhile. Operators can handle hardware issues on the spot and work around them, but what do you think happens with downtime due to non-deterministic software issues?