I think I know what they were worried about.
I have personally overtorqued AN3 bolts, so I know it doesn't take much.
If that prohibition against NAS6703 and AN3 bolts came from an organization that didn't control installation torque with strict standard practices, then they may have had failures and decided this would be the solution.
Another thing that makes it worse is that some flawed MS and NAS nuts have been on the market for a long time (even though they passed the specified tests) that led to very high running torque. Since the wrench torque is the sum of the running torque and the required bolt torque, you can see how the little #10 bolts are the most vulnerable. In these circumstances, the prohibition of #10 bolts in structural applications is prudent. For more information on this problem look for FAA SAIB HQ-14-16 dated April 2014. I suspect some of those fasteners made it into my organization's part bins at one time.
STF