Before you ask him to fix it, ask him how he plans on fixing it...and more importantly, how did it end up like this in the first place. Ask him what to do about the timing chain lenght issue? Ask him how out of round those bores will be? I'd stand there and watch him, because I'm willing to bet he's gonna go at with a flap wheel on a die grinder if you leave it with him, and while the thing might measure out OK, it won't be anywhere near round. Also, before you bring it back to him, bolt the rear cap down again and see if the thrust surfaces come close to lining up with those on the block. There is a lot involved in swapping caps and line bore/honing a block....you have to look at all of the things that can possibly go wrong, and have the "machinist" explain what steps he will take to prevent these things from occuring. If you're not happy with his answers, take your shit elsewhere. If he makes you feel stupid while you're asking him questions...take your shit elsewhere.
I'm not posting all this because I've had "experiences" with automotive machine shops, I'm posting this because I don't want to see you waste more time, and possibly money, and end up with something that's the same or worse.
I'd almost be inclined not to return the shop that let something like this out the door. The money you paid him...well, chalk it up to the price of education.
Understand that:
when they do work on the mains, they have to first machine a small amount off of the bottoms of the caps to make the holes smaller, but they also go out of round. After all the caps are torqued back on, the mains are bored, but you can't move a hole, keep it the same size, and keep it round, so the machining procedure involves an interupted cut, which encourages tool deflection, which makes the hole even more not round and screws up the finish. Additionally, with a boring bar as long as it needs to be to do the job, it too will flex. It is not a "set it and forget it" operation. It requires a real machinist who can monitor and make changes during the process to keep things going smoothly, not just a guy who knows how to machine stuff. This is why a lot of shops don't deal with main bore work...cuz it's a pain in the ass. The shops that DO still deal with it either have no clue how/are too lazy to properly do it, or are very expensive because all that attention to detail and time costs $$. And regardless of who does it, the crank centerline moves a little closer to the cam centerline every time you do it...so generally after having been done (especially poorly) once, it'll make a good boat anchor, since the timing chain will have enough slop to hook your shackle too.