I don't see why it would have a hidden automatic ISO increase. It reduces the light to the main sensor by 1/2 stop. The main sensor is used for exposure metering. It sees 1/2 stop less; it will set shutter and/or aperture based on the set ISO and the light it measures.
Actually, the ISO is based on what the sensor sees. If you point two cameras and a light meter and the same scene, all three of them should say (for instance) 1/125s at f/8 and ISO 100. It would be problematic if the SLTs underexposed in that situation. (Not that many SLT users will use an external meter or work with studio lights for shoot in M mode using "sunny f/16" but it would be an ugly exception if those methods didn't work).
So the cameras will ensure that when you set ISO 100, you're getting the right exposure, which amounts to an undercover increase.