Yes, exactly. Applying pre-RAW gain with no corresponding noise reduction benefit is worse than pointless; it's damaging to what the sensor if capable of.
Thought more about this, and while you are correct, raw converters and formats are not designed to handle an "ISO-less" camera, ie that the only effect of higher ISO is less exposure. The conversion pipeline will then show a darker image.
In order to show a 1 stop brighter image on the camera display when you go from ISO 50 to 100 and you need to scale the data. It would not be particularly hard to have a format with two clip points, ie if ISO 50 is 0 - 65535, ISO100 would be 0-32768 with "highlight recovery range" in the remaing range up to 65535. However I know of no raw converter or raw format that currently has this concept. There's only one clip point, and then if you do digital scaling (which you would if analog scaling would not give you less noise) you need to throw away that top stop. In practical photography that is normally not a problem, and if you really need to keep a huge highlight range than you just shoot at ISO50 and underexpose.
So I do not think it's a strange design, although the "two clip point" design and no scaling would be better for truly ISO-less cameras.
In the future I guess we will see ISO-less raw formats when the ISO is nothing more than a tag to hint the raw converter how to render the data, like white balance is today. But it's not how it's done with current and past formats, as far as I know. Hmm... maybe could be done in DNG with the BaseLineExposure tag, but I don't think anyone's doing it.