The support "IBM MQ Native" was productised in DevTest v8.1, after which time the previous "IBM MQ Series" support was deprecated, so you should always be using the non-deprecated version.
It uses configuration assets rather than putting all the MQ configuration in each response in the service image file, so it's more flexible and shares facilities with the JMS support. It also provides more flexibility for multiple response queues, direct queue definition, and other technical enhancements.