By auto exposure, I suppose you really mean any through the lens exposure metering , auto or manual.
My wife's new camera has the beam splitter and I put a linear polarizer on it and focused and metered in all orientations, distances and light levels.
I could not find a discrepency at all.
Than I chickened and bought her a circular filter.
But it makes me wonder if this isn't left over from earlier technology and now urban myth.