Kat it is perfectly reasonable to get your book set by a book designer/typesetter and take the finished product to a printer for printing, but the printer would probably want to specify one or two parameters.I know you don't need to get into the detail of Quark v Pagemaker, but in defence of Quark I found it easy to pick up, after starting on Pagemaker. It is far better supported, with a vast range of powerful extensions available, and version-for-version has outperformed Pagemaker nearly every time for 10-15 years at least, which is probably why it is the industry standard.
Quark's one failing was that it was slow to scope the PC market and create a Windows version, but they've had that sorted for several years now.
Lin may be a bit out of touch on print runs. With digital processes, runs of 400 upwards can be extremely cost-effective, b/w or colour.