I don't think there is another way to mount the Yamaha box.
The position of the two forward bolts on the rack forces you to drill.
I had no problems. Patience is the key.
This is what I did.
Tape the tail cone where you will be drilling like ionbeam said.
Mount the top box rack first to see where you will drill.
Mark the area where the two forward bolts will go.
I Used a very small drill bit first to get started (about 1/8 "). Then I moved up to 3/16"
Then I used a flashlight to look through the hole to see my positioning (as per the link provided above).
Use a Unibit, or if you don't have one, move up in drill bit sizes until you get the right size hole.
I didn't have a Unibit, and if your Unibit is too long, it will not widen the whole enough before you hit the threads where your mounting bolts will screw into.
Finish the hole with something like this,
No marks, no scratches, no problems. Use threadlocker blue on the bolts.
I have never taken the rack off, and don't see a need to.
Nobody can see under the rack anyway, but it cleans up nice.
No problems after almost two years.