That's a really annoying problem caused by the OIF frame designer not considering all the clearances at the time! Its really frustrating.
The best solution I have found so far, is to sort it out when the primary chain is out of the way during a clutch stripdown. Take the bolt out and when screwing it back in, place the seal and a very thin locknut under the chaincase to 'catch' as the screw goes down. It's permanent until the next stripdown so I use a Dowty Seal. It still doesnt seal all that well, but without, it leaks out.
The alternative without stripping down is to file a big flat on a Dowty washer and file down so it will just pass the frame tube. Then make a special 'long' nut from hex bar, turning a portion to a diameter that will allow the nut to pass the frame tube, but short enough that you can grip the flats on the screw to hold in place whilst tightening the locknut - and leave enough exposed thread so the end cap and a seal can be fitted.
Unless someone knows a better/easier solution of course......
Chris