I have some xUnit tests which are failing with the common
Could not load file or assembly \'FSharp.Core, Version=4.0.0.0, Culture=neutral,
PublicKeyToken=b
By using NuGet, I added FSharp.Core.3 and it fixed my issue.
I don't know xUnit, but if your unit test runner supports app.config files, you can just attach the config to the unit test assemblies (e.g. an app.config along the lines of what you get with a default F# console application template). If the test runner does not honor app.config, then I think the machine.config strategy is a decent one.