I am using foundation bolt connectors in my model of a gearbox bolted down on a concrete foundation. However, I notice that there is no opportunity to specify the length of the foundation bolt. Is SolidWorks Simulation assuming the length is from nut contact surface to the virtual wall?

Foundation bolts are longer than that distance. They are embedded in the concrete. A shorter bolt is stiffer than a longer one of the same diameter. If only the nut to virtual wall distance is what Simulation is using for the bolt's length then it will be much stiffer in the model than in actuality. When you have a preloaded bolt the additional load on the bolt depends upon the relative stiffness of the bolt and the joint. The calculated load on the bolt will be wrong if you cannot account for the length embedded in the foundation.

Do you agree with my statements above?

My next question is how would you get the forces in the foundation bolts if you did not want to model the foundation too. I am thinking of making a plate where the foundation bolts end, put holes coincident with them and using regular bolt connectors. I would make the plate rigid to reduce computing resources. I will be trying this later. Any other ways you would suggest?