It wouldn't be out of line to ask those questions. After all, it's your money and your engine. In my experience balancing is generally treated as an extra service. Parts are refurbished when possible and economically feasible. Connecting rod bearings, main bearings, cam bearings, camshaft and lifters, and rings should be replaced. It's rare to find an engine with many miles on it that doesn't require cylinder boring and piston replacement. Crankshafts can usually be ground and proper bearings installed. Connecting rods will need to be resized and bushed. Valves and seats can be ground if not too worn. Valve guides should be replaced. Line boring isn't always required but should be checked. New oil and water pumps are cheap insurance. Detailed paperwork should be supplied and any parts that were too bad to use should be returned. The machine shop may have a source for parts other than the ones you mention so it wouldn't hurt to ask them.
I used the same couple of machine shops for the last 40 something years. One of them was a one-man operation and we became close friends over the years. Sadly he passed away last year so I'm stuck with one local production shop that I trust. There are some local specialty machine shops but they're more committed to commercial customers. I've had work languish for months at those.
Good luck!!