For me the question would be if "ignore" really has some special interpretation or not. If not, enemies are either fortified or they are not fortified and since you ignore site fortification, most enemies will not be fortified.
You could argue that they are fortified, only YOU ignore it, i.e., you can play ranged attack against them, but I am not that positive you can pick and choose like that, it just makes the game more complicated.
What you CAN do is use timing, to play stuff like Earthquake and then remove fortification, but as you pointed out already, you have to play Underground Attack first.
I would currently rule that once you play Underground Attack, site fortification is not taken into account, i.e., most enemies will not be fortified and that is the end of that :)
You could argue that they are fortified, only YOU ignore it, i.e., you can play ranged attack against them, but I am not that positive you can pick and choose like that, it just makes the game more complicated.
What you CAN do is use timing, to play stuff like Earthquake and then remove fortification, but as you pointed out already, you have to play Underground Attack first.
I would currently rule that once you play Underground Attack, site fortification is not taken into account, i.e., most enemies will not be fortified and that is the end of that :)