There's enough clearance between the bolt head and the bottom of the pulley to get a Vise-Grip in and grab the bolt head, so I suspect a cap head bolt will clear the pulley.
Although as I think about it, I probably need a washer under the cap head, but even with a washer I suspect the clearance won't be an issue.
I'm wondering is all the slop is there to protect the aluminum casting of the spindle. Although the square holes do get chewed up with the carriage bolt spins, so I have no idea what the Deere engineers are thinking. It's real mystery.