Thank you everyone for your input. I never know if these issues are fairly typical or something to be alarmed about. Hollysprings-We had issues with the bathroom floor being unlevel. The GC, cabinet maker and tile setter worked together installing the cabinet. Maybe that was the best they could do with that crazy floor? Enduring- I see shims and will follow up w GC to ensure there is adequate support. Thank you! Hosenemesis- There is caulk near the walls, but no caulk in the middle of the counter where I see the shimmed area with the big gaps. I sent the cabinet maker a pic. Will follow up when resolved.

The backsplash will more than cover 3/8" . Most thin tiles are that by themselves. Thicker tiles can be 1/2" or more. Then the thinset is anothe 3/8" at least. Don't sweat it and leave it alone.

three leaf clover: Check your countertops for level. Install plastic non-compressive shims if not. Place a continuous shim the thickness of the grout line on the counter. I've used 2 rips of 3/4" wide plastic laminate with great success. You may want to dab some hot melt to hold it in place. Adhere your tile to the wall, starting by placing the first row on the shim. Tile as high as necessary to get where you need to be. Grout the tile, then pull the shim and push color-match silicone into the gap.

The side splash is 3 cm thick and appears to be of a different slab/year (the veining is less white and less crisp/no small veins). Can it be milled thinner? Every inch counts in this kitchen. Black caulk might look better, am concerned about the fridge panel getting damaged at this point. And the bead of caulk doesn’t extend the inch past the cabinets/sits on the white cabinet. Photo of the other side for context. I am paying nearly $3000 for a 8x9” galley. MSI marquina midnight. We thought we might tile the backsplash eventually so asked for scribed to the wall as though we’d do no backsplash to give us the most options. Also, MSI minimum radius is 3/8.” Sink is still a little offset from cutout, silicone seeping out, cut areas a bit duller finish than gloss areas).