to the OP:
Any chance there is a large distance between the open ends of the pipes and that something else is going to go into that area? As in gates, sorters, joiners, temp controllers, pressure controllers, things like that? That's such a large offset that it almost sounds intentional. But, if he says it's "normal", like you said, IMO something's rotten and it's not in the dirt underneat the concrete.
That camera idea's a very good one. Get pics from a couple of different angles of each misalignment, and carefully note the location in writing right on the pic. Let the builder know you did it. I'm no expert but I think I'd also insist on having the contract modified to specifically incluse any damage that might arise over time due to this issue so that it cannot be attibuted to "an act of God" or some such thing down the road. If he's a good businessman, he'll likely give you as much of what you're asking for as he feels reasonable. That will tell you a lot.
Actually, I think the best thing you might do would be to get those pics and then see if you can't get an inspector or city engineer, whatever, to come out and look it over. They may or may not have some interesting comments, but either way it's going to help settle things a lot. If you can afford it and they city/town whatever doesn't have one, you might even consider hiring a structural engineer to take a look at it. Don't stop the contractor from working or you'll get into contractual problems. But don't make any secret that you're questioning the misalingnments either; he should have nothing to hide. In fact, maybe it was one of his subcontractors at fault, if there is a fault, and he might be more helpful than you think. Or not.
I assume you measured horizontal misalignments. Are there also vertical misalignments? You might need a level to figure that out.