Ok, just looked again. Since the Royal Palace in the Viking campaign replaces the Mead Hall, it isn't adding another valour. Its just saying it still adds the 1 from the previous upgrade. And it just does it for the faction specific Infantry like Kerns/Gallowglasses or CelticWarriors/etc... Like with the Horse Breeder, the 3rd level upgrade says Valour +2 and adds 2 valour, not 3 for the first upgrade and the second.

It doesn't seem to add to the Royal Bodyguards/Emissaries even though its the building that enables them. I'll have to check if the stables bonus does go to them, but I don't think it does. So yeah, its kind of odd and confusing. As for the generals, there is a way to have them lose some stats when dieing.

Add -green_generals to your shortcut(just add it after the -strictserver line) and they will slowly deteriorate after each death. Requires you to keep an active general unless you want him being half useless in 80 years.