[PvK]

No, as long as you use a ship design of an alien race, the simulator will use that race's actual combat bonuses, at least as far as the displayed percent chances to hit go.

Experience and system-wide modifiers are two things the simulator doesn't take into account. However it does seem like it does something wrong at some point, but I'm not sure what it is either.

I think it might be something with using "Auto", or with telling it to resolve the entire combat. Or, it might be that although it displays the correct percent chance to hit when running simulator ships on manual control, the actual resolution of fire is done with some bug in it (like, throwing out the racial mods). I dunno - it could use further testing.

PvK