The chain may be parallel to the rear sprocket for the time being. The axle may have been adjusted to compensate for a potential 1/8" out of flushness caused by a chain not being centered on the sprockets. Ride the bike, the chain will move left and right on the sprockets and it's not aligned anymore.
You might get the chain aligned perfectly using the swingarm marks and then second guess it almost an eight inch out of alignment using that tool.
Same goes for the alignment tools with cones that fit in axle hole and swingarm pivot hole. The busa has a much smaller hole on one side of the swigarm pivot than the other so the cones can't fit the same on both sides even if the alignment is perfect. Not to mention there's no law of nature stating the swingarm pivot must be parallel to the countershaft. It would still function as needed if it were off by a few degrees.
I think I'll just stick with my method.
Tighten the locknuts up to head of the adjuster bolt.
Thread both ajuster bolts all the way into the swingarm. This is your zero mark, the farthest point the axle can be moved forward. If anything about the OEM swingarm is identical on both sides, it ought to be this. If the axle is placed here, the rear sprocket will be aligned to the front. The chain will have a perfectly straight path to follow around the sprockets.
Count the number of rotations/flats required to adjust the chain to the proper tension. The rotations/flats must be the same count on both adjuster bolts so that continuity is maintained with the zero mark on both ends of the axle. Both adjuster bolts have 1.25 threads/millimeter. One rotation = 360° = 0.8 mm in or out on both sides. One flat = 60° = 0.2083 millimeters in or out on both sides. It has to work if you believe thread pitch is very accurate and assuming the zero mark is aligned with the countershaft as it should be.
Loosen your locknuts off the heads of teh adjuster bolts. Thread the locknuts up to the zero mark and tighten. Tighten axle nut and the chain should be should be darn near perfectly aligned to the sprockets.
Total pain in the arse to set it up initially but after that, you only will be turning one flat each time you adjust your chain tension until the chain is worn out. Forget the damn marks on the swingarm, just count flats. Mark the flats and make sure you don't screw up clockwise and counterclockwise!! This worked flawlessly on my ZX-14. It also seemed to correspond to the swing arm marks. When I finally got right on one, the other side was right on too. The wear on the rear sprocket and the front sprocket was equal on both sides so that chain was running straight. I used this technique on my busa too and we will see how the sprockets look when I change them soon.
Now if this method ever fails, then I'd say it's time to try a special tool.
The Motion-Pro tool is always going to indicate straight unless you have a lateral kink in the chain like Rubb said. You clamp it on the chain, of course it will be straight with the rest of the chain if the rest of the chain isn't bent laterally. I'm smellin me some snake oil.