Apex has a Transaction Control system for rolling back changes to SObjects. Are Custom Settings included in a rollback? (To be more clear, are Custom Settings reverted to the state that they were in when setSavepoint() was called?)
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Yes, they are. In fact changes you wouldn't think of as DML are also rolled back: calling @future method, sending email, and others. In essence outside of the current apex state rolling back undoes EVERYTHING you did.