After lots of searching, I think I finally worked out how to use #Godot's Version Code and Name fields...
The fact that the Code is an integer was confusing, as I'm trying to use semantic versioning. So in order not to have random integers assigned to my semver Name, I set the integer to the same as the semver name, but with the dots removed. Therefore v1.0.1 = 101. Hopefully this works going forward.