Where are the speaker wires they ran? Built-ins with speaker wires behind them should of been put together with the speaker wires coming out through a hole in the built in somewhere.
From there, you would get some bookshelf speakers... and put them on your bookshelf!
Even if you can only set it up as a bookshelf stereo setup, it will sound far better than any speaker bar you could possibly get.
I would figure out where those speaker wires are which you paid for and talk to the builder if they got buried in the walls somewhere behind cabinetry. Make this THEIR issue, not yours.
Communication is key in all of this. You shouldn't need to raise a stink about it, but just let them know you have an issue, what the issue is, and have them deal with it. You should also talk to us about your expectations so that we can help you ask the right questions and make the right complaints.
If you bought a surround sound prewire, then ONE HDMI CABLE IS A LOUSY MOVE ON THEIR PART! They should have run 2 HDMI cables and 2 pieces of cat-5e from the equipment location to the TV if the wires run through joists. They should have run 5 speaker wires throughout the room for surround sound and one coaxial cable for the subwoofer (5.1). This would be the most basic wiring that should be acceptable for a theater 'package' as they call it.