Answer:
By default, the Shear plane in thread option is activated and the lower strength according to the selected design standard is considered for the bolt shear check.
In AISC, the bolt nominal shear strengths are listed in Table J3.2. As an example, Group A (for example, A325) bolt has a nominal shear strength of 54 ksi (372 MPa) when the threads are not excluded from the shear planes. To use the higher strength of 68 ksi (469 MPa), the option can be unchecked to exclude threads from the shear planes.