Natural stone needs a much stiffer subfloor than does ceramic or porcelain, thus more prep. It's more difficult to lay and needs different more expensive setting materials. Yes, it's usually 40-60% more expensive to lay than ceramic or porcelain. It is NOT "the same" material as ceramic or porcelain.

The subfloor extra cost may apply to a wood subfloor but certainly not to a concrete slab. Even with a wood subfloor it seems a bit cheap to build a weaker one for non stone tiles.

Mortar bleed through is an issue with stone tiles but it's in the vicinity of a few cents per sf for the stone compatible mortar.

Stone tile is cut with a wet saw, which is more work to set up and clean vs. score and break.

40% upcharge includes a luxury labor charge because if clients are willing to pay for stone, it's likely they part with money a bit more freely than clients with a tighter budget who chose ceramic tiles instead.

Plus, it is a change order.

"Our tile quote went up a huge amount even though we did not change the materials, sizes, or designs of our spaces."

But you did change the materials!

We did not change the materials. The materials were on-site at the time of the estimate. We have no idea why he quoted for the wrong materials. There are areas he quoted for the right materials and added a huge amount to his updated invoice even though not one element had changed.

Natural stone is always more expensive to install than porcelain. Read the contract to see what you were quoted for what. If it doesn't specify natural stone tile, then it's a change order. It's back to your GC. He should have read the bids from the subs and determined that they incorrectly bid the job based on incorrect materials. If your contract with him specifies natural stone, then he should eat the overage. If the contract only says "tile", then the "changes" are on you.

Yes it does ;). If he quoted the wrong material, that is not your fault but still if the material quoted is different from the material to be installed, the price will go up.

Stone is much more expensive to lay than porcelain, for a variety of reasons.