Currently PCDMUse just uses warn to output its warning about PreservationMasterFile, which means there's no good way to silence it or format its output. If we used Valkyrie::Logging this would send the warnings through the same output and formatting channel used for other logging.
Alternatively (or in addition?) we could use something like @cbeer's deprecation gem (cf. Blacklight), which both makes it possible to configure deprecation warnings separately from other things, and uses a logger (an explicitly configured logger if there is one, or the Rails logger if available, or a fallback logger if not).