You know that little "make a wish" button at the bottom right when you're logged into Meraki? I'd press that and put in an enhancement request. It wouldn't hurt to open a case as well with the enhancement request. I would love to see Meraki support flexible NetFlow as well as the ability to have multiple NetFlow destinations, and different flow records.
Full disclosure, I'm a Cisco employee, but don't work in the Meraki Business Unit. When I worked in the Stealthwatch BU, we were always looking for customer input to make our product better. It isn't possible to do everyone's enhancements, but with network visibility being a huge play at Cisco, this one might get attention. Meraki is pretty responsive, but this might be a big request.