I don't think your model as it is needs to be rotated but I think it should be translated to BobCAD 0,0,0 UCS. You can override how your STL's were "saved" in relation to the UCS and move them around in the Machine Definition but after experimenting with my own machine models, it's better if the center and face of my spindle is always at X0, Y0, Z0, the same as it is when I push "Home G28" on the Haas or line up the CS (Zero) position of my Fadal. Of course both the Fadal and the Haas allows for a "Home" position different from Machine Coordinate Zero, but I made a decision several years before we even purchased CAM software that I would never do that just in case I get full Simulation. All axis set to Zero in Simulation (right click the Axis controls, set to Zero) should look just like the real machine when it is sent to "home" when looking from the top of the machine. Again, I say should but I don't believe it is absolutely necessary, it's whatever you want. I want it EXACTLY like my machine.
You can stack as many geometry files as you want on an axis in the Machine Definition. I haven't investigated whether this makes your Machine in simulation occupy more resources but I believe it would. Like the MDF spoilboard on the top. If you lump the table, vacuum plate, and spoilboard all together, is that STL smaller than all three STL's individually loaded into Simulation? I would think it would be because lumped together you don't have the faces (and the little triangles that make them up) in between.