org.apache.pdfbox.preflight.PreflightConfiguration#getInstanceOfProcess(String) method is supposed to return a validator instance for given process name. If process is not found (is not set in PreflightConfiguration) and errorOnMissingProcess flag is set, an exception should be thrown. If that flag is not set, an instance of NOP validator (org.apache.pdfbox.preflight.process.EmptyValidationProcess class) is returned.
Unfortunatelly there is no way to unconfigure (i.e. disable) specific validation process in PreflightConfiguration. Though it contains the methods #replacePageProcess(String, Class) and #replaceProcess(String, Class), if null is given as the second parameter specifying validation class, then #getInstanceOfProcess(String) method fails with NPE instead of expected behavior for missing validation process.