Wait... you KNOW, how the Imperial Geographical Society measures all mountains and islands... that is very interesting. I wonder, what technology do they use to measure the depths of the waters surrounding Vvardenfell and how they get to those depths. In any case, no one said it was the tallest mountain, they said it was the highest peak... that really doesn't have anything to do with how tall the mountain is from its base and everything to do with the altitude of the highest point.
Of course I don't know for sure but I'm going off of the facts presented, and the only other knowledge I have on how mountains and islands are measured in real life. As far as technology, how can you be skeptical of the societies ability to measure below sea level when the use of magic is so common place and water breathing spells and enchantments are readily available. After that it would be a simple task to measure the same way down as they would measure up. I did not dispute the fact that Red Mountain is bigger, and since no source is truly clear on HOW Red Mountain is bigger neither of us can really make a compelling case for any specific argument. I gave my views. You clearly disagree and that's fine.
(EDIT) "This is the highest mountain in Skyrim, and the highest in Tamriel aside from Vvardenfell in Morrowind." This is the best information we have on knowing that Red Mountain is higher, but since we don't know where the measuring is starting it's still vague and it could be that Red Mountain is measured the way I say it is, or they are both measured beginning at sea level which would also mean that Red Mountain is taller still than High Hrothgar. For all we know, High Hrothgar's measuring could begin at the first of the 7,000 steps to the top.