I imagine most the snags you've mentioned will get addressed with silicone.
That wouldn't be acceptable to me. Some of the tiles have chips on the edges, siliconing those will just look an absolute bodge. The same really with uneven cut tiles - surely common sense says to put the side that you're cutting against the wall, and then the adjacent tiles that don't need to be cut can then be fitted flush.
@LeeUK i would make sure you hold back enough that you can pay another bathroom fitter to do the remedial works if needs be. There was another story on here of someone who had a downstairs bathroom toilet fitted and had paid something like 95% of the bill and the guy never came back to finish the works/deal with the corrections for the sake of something like £100-150. Which means they were never going to find a new fitter to rectify the old fitters mistakes. The last thing you want to do is fork out for more cash to pay for another fitter to essentially redo everything.