However, thanks to how the industry is regulated, Boeing don't take chances if there is a risk to passenger safety. In this case, the likelihood of a single engine shutdown due to this elusive bug + the failure of the automatic restart system + the failure of the manual restart procedures, _combined with the fact that all commercial aircraft needs to be able to operate with only one of the engines_, makes Boeing ask for the exemption.
The FAA, on their part, is 100% right in demanding that Boeing show their work and is unlikely to grant such an exemption unless the risk is calculated to be negligible.