Does not really solve it though. I mean Ishamael would have had no way of knowing that Rand would start a male channeling organization and that due to LTT's influence, he would not visit the place at all and as a result let a darkfriend corrupt the whole thing. As far as Ishy would have known, any significant construction would happen far before the last battle, and as such any usage of SG-stone would have to happen far before LB too.

So if he had no idea that there would be a BT, he should realistically have "used up" the quota of SG stone far earlier, such as during the trolloc wars or somesuch, and probably on the White Tower/Tar Valon or maybe major cities such as Tear or Caemlyn or such that he would have expected to play a major role in the end.

So basically, if there is a limited quantity of SG-stone, there should not have been any left for BT. Heck, even if Ishy had a prophecy or something, using it for BT would be a poor choice regardless. I mean thanks to Taim, the BT is totally corrupt and does not really require any special SG-stone properties. Major cities or the White Tower on the other hand are not totally under shadows control, so if SG-stone gives the DO power over a place, it would be far more usefull in such places rather than in a place that belongs to the DO anyway.