After letting Meraki-support enable the NAT-exemption feature, you can selectively disable NAT per WAN-port and even per VLAN.
Works good. With one customer I habe a direct internet-line on WAN2 with NAT, but on WAN1 the ADSL-router in front of the MX is doing NAT, so I disabled NAT on that port.
You probably don't want to have the "Meraki Passthrough" mode which would work as a L2 bridge on a single WAN and routed mode on the other? That is not supported.