applySettings should return new pb.Settings

[wasaga]

          in fact, we _used to_ merge with current settings, but we don't anymore. as a follow-up we should update the applySettings function to explicitly return a new pb.Settings rather then taking it as an argument, that is a legacy of previous behaviour where it merged changes into it.

Originally posted by @wasaga in #811 (comment)

[calebdoxsey]

I attempted to do this but I don't understand the requirements. There is no applySettings function. There's an ApplySettings function in core but it neither modifies nor returns a pb.Settings object. There are several applyXXX functions that could be modified to return new pb.Settings objects. I don't understand why we would want to do this, but if that's the ask I can make each of them use proto.Clone and return a new pb.Settings object.