Let's say a certain amount of light is entering the camera. The proper exposure is determined to be ISO 100, f/8, 1/200 sec. That represents a certain LV (light value). If we agree that it is the proper exposure, then any other camera which can take a decent photo will decide on something equivalent to this. It may be that the D40 (whose "native" ISO is 200) will choose to go with ISO 200, f/8, 1/400 sec, or perhaps ISO 200, f/9, 1/200 sec, but either way, those are all still equivalent to the same LV, and hence the same exposure. The ISO changed, yes -- some sensors have different minimum ISOs (which may have actually been the case here) -- but of course the aperture or shutter speed also changed, to allow the same amount of light in.
If a full-frame sensor (for example) is more efficient at collecting light, then its calibration (what exact level of sensor gain will correspond to "ISO 100") will be set so that ISO 100 is ISO 100 is ISO 100, as it is written on the stone tablets of the International Standards Organization.
I don't know what else to say -- the details of exact sensors have NOTHING to do with what ISO 100 is. Some sensors are better at collecting light, there is no doubt -- but then the cameras are calibrated to take this into account, so that there are no surprises about what exposures are appropriate in different circumstances.
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