I agree with your observation that a lot of machine shop work is based on a get it done philosophy. As an example, if one wants to bore a hole for an SAE thread, you can calculate precisely the diameter for whatever percentage thread you want, go to tables, of use the simple shop equation of screw nominal diameter minus 1/tpi. Thus, the hole for a 5/8-24 thread becomes 0.583. Machinery's lists an acceptable range of 0.580 to 0.585. I don't know of any substitute for a good machinist teacher.
As a note of caution, my perspective is based entirely on using manual machines. Aside from just talking, watching, and doing, the source I use first and foremost is Machinery's Handbook (Industrial Press). It has good sections on materials, strength of materials, engineering equations, machine practices, and tolerances. In 1983, I used that handbook and a little common sense to design this 50X18 foot door. I built it using mostly TIG welding, and it has withstood the elements and winds in Minnesota.
For "how to" books, I use Machine Tool Operations (William Patton, Reston Publishing company, 1974), which is very basic, and Milling-Machine Practice and Work (I.C.S. Staff, International Textbook Company, 1927). The latter has nice descriptions of complex manual milling operations, like spirals and cams. I also find that some of the tool catalogs, like J&L, and even McMaster Carr have useful information. I suspect more modern books are available, but with dying of the trades and trade schools in the US, they may be getting hard to find.
I
rarely go to the Internet with questions, because there is so much noise in the responses. The "DIY-CNC" group in Yahoo Groups is interesting to follow.
Good luck.
John