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> However, if you were interviewing with a .NET team before June 2016 even asking the question "What operating system will this run on?" would have been a sign of incompetence.

It really depends on how you're asking the question. "What OS will this run on?" is going to be perceived differently from "Are you expecting anything unusual like Mono support?".

The OP didn't actually say that this was a .NET application, but if it was the answer to either question would have been important. If the answer had been that the company expected a standard Windows environment, I don't think it's likely that the second question would be perceived negatively.