I don’t need any of that between sites, and never will, hence I won’t search for a solution for something that I don’t need.
I only rely on L3 between sites.
Probably there isn’t a better solution to what you’re trying to achieve: http://forum.mikrotik.com/t/wireguard-and-eoip/154495/1
But still you can’t ignore the fragmenting.
I did some tests a while ago with proper MTU set in wireguard and .. not, the performance drop was terrible with bad MTU, no L2 bridging is worth that.
And it’s not something MikroTik specific, there isn’t any magical solution to your “problem”, there will be fragments.