I think it's because the bike is elevated at the rear in the photo. It has more rear suspension travel, and the seat is located higher, and nobody is sitting on it.
I can tell you that no tranny movement was used in terms of the connection to the engine, because Chumma would have had to do that. Chumma built this engine and made most of the primary chaincase modifications. He did not do any indexing of the bolt pattern that mounts the primary to the engine, or change the stud holes to mount the gearbox, or anything like that.
I think if someone was sitting on the bike to take out the spring preload, then it would look more oriented like we would expect to see.
A close look will reveal a fully shrouded lay-down longitundinal coil-over monoshock under the engine, which is articulated off the bottom of the swing-arm.
The exposed clutch and back part of the primary chain are real pants-grabbers. I think this is really made to be a show bike, or else very tight pants and judicious foot placement would be required.