Demote Giraffe warnings that users can't fix to notices

[adamnovak]

As in #3369 (comment) we sometimes get users complaining that Giraffe is spitting out warnings. These are actually really for people who are tuning the mapping parameters, and not things that a person who is running the tool with a recommended workflow actually needs to do anything about. Importantly, you are expected to encounter some of these even if nothing has actually gone wrong.