You are correct that those are edge choices, not stone thicknesses. If you purchased a 6cm built up edge, he needs to remove the island top and redo it. Your contractor will need to build up the island subtop by that 3cm and take into account the consequences of that extra counter thickness, like the additional counter height that it adds to the design. Overhang supports are created in the design phase and installed by your cabinet installer. That is not the stone installer responsibility. Support must happen before the template happens. 3cm needs support beyond 10”, so yes, you'll now have to retrofit something external like L brackets with braces, and likely reinforce the cabinet interior to accept it. Or, if the island is getting redone, that’s the time to have the designer reengineer the support correctly. Which they should have already done.

If your edge is stacked, it's some sort of adhesive bleed apparently. Acetone and paper towel poultice to start.

Resin pooling is a feature, not a bug, at least according to the manufacturers. They can be drilled, filled, and polished.

Search on this forums for "quartzite staining" in Discussions. You will find that this is a common problem with these white/gray quartzites. There is no real fix. Several here have had to replace the counters after unsuccessful attempts to get rid of the stains.