I know Porsche had some growing pains with the 919 platform, but I don't remember anything about the format of the engine posing problems?
The top candidate is the Aprilia RSV4. The Honda VFR 1200 is quite interesting because they've worked out an extremely smooth running motor without a balance shaft which would lend itself well to solid mounting and features a dual clutch trans and already has shaft output but would otherwise be a weird fit in a car application and require a lot more reverse engineering to drop the cg closer to the floor.
I discovered one application of the RSV4 in a car: http://griiip.com
a little after finding it might have potential, if for nothing else than sound. Griiip seems much more interested in selling the G1 as a racing package than as a car so they aren't very in depth with their descriptions of how the thing is engineered but i am most curious.
I'm possibly in a small group, but i never liked the sound of a flat engine.