What does he say about the uneven tile spacing (gaps)? Why does he say the tile chipped? Probably a dull blade and did not use spacers for the tile. I would not allow him to get away with this but the waterproofing may end up being compromised when removing the tile. What sort of waterproofing system is behind the tile? Him thinking the above work is acceptable makes me wonder about his ability to properly waterproof the substrate.

He's not wrong that there are sometimes tradeoffs to be made when laying out longer tile in a bond pattern. But the argument doesn't make much sense here--looking at your photos, if they had shifted the pattern over slightly to eliminate the slivers on the right side of the niche wall, it would have benefited the smallest pieces at the edge of the niche. And on the wall with the plumbing, they should have started with whole tiles at the corner. I can't see the other end of that wall in your photos so not sure if that would have left you with slivers on the other side. But based on the layout visible here, it looks like that wall turns a corner so a sliver on the other end would have been preferable visually since that wall seems to be more visible than the smaller corner on the left side of the plumbing, which you'll only see from inside the shower if you happen to be looking out. The wall to the right of the plumbing will be visible from the main bathroom, it looks like. So again, tradeoffs might have been necessary, but it doesn't sound like they consulted you on it. And honestly, with tile this long you can also fudge it a bit and not have the pieces wrap the corners perfectly proportionally--e.g., you don't have to go from a 6" piece on one wall to a 2" on the next simply because it's 8" tile; you can wrap to a 2.5" or a 3" piece if it eliminates slivers and your eye will think it's right because it's close enough. Not sure there are many remedies at this point, unfortunately. Caulk will probably hide the very skinniest slivers, but not the bigger ones. You could potentially put a corner shelf in to cover some of it, but it doesn't look like you need one with the niche there. Fixing it in any more substantial way would mean ripping it all out (and probably starting from scratch since I doubt you could do that and keep the waterproofing intact).

When counters and cabinets are not level, and you have choses an irregular handmade tile, nothing will line up. This is not an A+ install. It is very far from an F. Remove the grout at changes of planes, and caulk, and it will be a solid B.

The one thing that could have been done differently would have been to use a piece of solid surface material on the bench top (granite, quartz, corian). Easier to keep clean, specially with wavy lines going side to side and not in the direction that the bench should be sloped, which should be back to front.