HMRC recently answered this question in the following manner:
Will customers receive penalties for not filing MTD returns or keeping digital records?
Not yet. The government has confirmed a light touch approach to penalties in the first year of implementation for MTD VAT. Where businesses are doing their best to comply, no filing or record keeping penalties will be issued. However, customers must continue to pay their VAT obligations on time, as late payment penalties will still apply.
MTD Developer Update: April 2019