Glad to hear the runtime is faster. Hopefully that will hold up!
Regarding the warnings you are getting, those are coming from the BSIM4 device model and they are part of that model, as the original Berkeley developers designed it. In the more recent versions of Xyce we modified the code to throttle warnings so that you (hopefully) won't see too many of these. But basically, some internal parameter is evaluating to a value outside the allowed range.
I should give the caveat that I haven't run Sky130 much myself.
I have seen other people report seeing these warnings from Xyce. If ngspice isn't emitting these warnings that could be a sign of something we need to fix. Sometimes, I've noticed that various simulators have extensions to models like the BSIM4, that go beyond the original Berkeley code. So, that could be a potential culprit. If that were happening here, you'd probably see some warnings about unrecognized model parameters. Are you seeing any "unrecognized parameter" warnings as well? If so what were they?
thanks,
Eric