Hello Guys
In the implementation of Cross NSX 6.3.5, we have configured in both MTU 1600 sites at the Switch Core level, but the connectivity between both sites (MPLS provider) only delivers MTU of 1500 between router.
The L2 VPN solution described starting on page 19 of the Multi-site Options and Cross-VC NSX Design Guide.pdf is the only currently supported option to extend networks between the sites without at least a 1600 byte MTU. In my experience there aren't many MPLS providers left that can't accommodate jumbo frames upon request so would definitely encourage you to explore that with your service provider as a first option since L2 VPN still doesn't allow you to take advantage of things like the UDLR and isn't as easy to manage/implement as true cross vCenter logical switching.
For your reference.