1. If the design is so preliminary that the number and location of the fasteners is not yet fixed, then defining a joint between the mating surfaces seems like a good idea to decide on the total number and a rough initial sizing.
  2. After the number and locations has been decided, add nominal holes at those locations and create a Fixed Joint at each hole pair. Some Joints will carry more load that others. Sort the loads to find the hole pair that has the highest axial force and the highest total shear force. Now you can use those numbers to make a final selection of the fastener size.
  3. The force going through the Fixed Joints will not be significantly different between the rigid and deformable behaviors, so for bolt sizing you can use either one. However, if you also want stress output on the mating parts, the rigid behavior is more likely to create a stress concentration artifact compared with the deformable behavior.