They're still figuring out how to administer the program. Wait until the folks who bought one and leave it hanging in the windshield day after day find that the sun fades the printing and they have to buy another....
You might try being inventive. Maybe photocopy the pass, write your cell phone number on it, and tape the copy to the bike, or...??? The same problem you describe arises for jeeps and such with no top. Maybe telephone the office of the place you're planning on visiting and ask them how they want you to proceed. Note the date & time & full name of the person you speak with, so your letter to the judge about the citation will have full details.
Does everyone know that if they've bought the federal America the Beautiful – National Parks And Federal Recreational Lands Pass, there is a free annual sticker available for motorcycles and other vehicles without a lockable cab? Most of the federal offices that sell the pass also give out the sticker, but check first. The sticker expires yearly even for those of us with the lifetime geezer pass. You'll need the pass, your photo I.D., and vehicle license number to get the sticker. The sticker is valid in parking areas without an attendant. If you go through a gate with an attendant, you'll still need the pass & I.D.