I don't really see it as a big deal either. The T-Stop issue has been with us for ever. In fact I think it's true that no fast lens is actually as optically fast as it is marked for several reasons, first absorption by the galss and second vignetting. In the days of film it was not at all unusual for images shot at full aperture to be slightly uderexposed when compared with those shot stopped down a stop.
Do manufacturers boost ISO when they know they have a T-stop issue? I don't know. I suppose it would be nice of them to tell us if it was true. You could test this theory by using a manual focus fast lens which wouldn't tell the camera what the actual aperture was and so the camera couln't compensate.
Either way I don't see it as a big deal unless you have a bad case of what has been called "measurebation", i.e. an unatural or excessive concern with measuring things that actually make little difference in practice.
Lens makers lie about focal lengths, they lie about apertures, camera makers lie about ISO speeds. Well, it's true if "lie" = "stretch the truth a little". Specs are designed to look good as much as to be accurate. There's always a +/- 5% or 10% factor and the published number are always on the side of that range that makes the product look better. So your 400mm lens may actually be 380mm. It's never 420mm.
It may be useful and interesting to knpw what's going on inside a camera and lens, but in the end to an actual photographer who's main concern is the final image, it's typically not very important.