Ok, so I'm always looking to spend all those cellar stones in another building or something. Like the stone tower which requires so much stone - cellar stones seem perfect for that to me, if the color is right.
First I was going to suggest to just count the amount of the stone under a specific building as already pre-built into said building, but then I remembered that the stone type might be of a color no one would want.
Then I thought that you might remove the amount of stone available from the cellar of the building you're trying to build from the total building costs and just have cellars "pre" dug out for that amount after placing a building sign. It would ensure that there's no color clashing but it would also leave us with an issue of what if there's ore/coal under the building? Personally I wouldn't mind this cause if you're plopping a house on such a node, your fault.
But let's say that's not an option - how about some sort of survey-like thing where you actually have to construct foundations for a building instead of just normal paving? So you could actually take out the stone first, build the foundation and upon that build a house and choose whether to use that stone or not.
Obviously it's a bit of a complex idea that warrants more discussion and thoughts, feel free to opine and I'd love to hear from Jorb or Loftar as to how much of an effort something like this would require on their part.