Do Professional Manufacturers Violate IPC Standards?
IPC rules don't really depend on the PCB manufacturing process. They're mainly about the PCB assembly process.
The recommended pad sizes ensure there's enough solder paste to hold the component in place. The toe-room ensures a good solder fillet can be formed. Overall they provide very generous allowance for placement tolerance.
The courtyard mainly makes the order of pick and place operations not matter (you don't have to worry about programming the small parts to be placed before the tall parts), and ensures enough room to fit a hot-air nozzle around the part in case re-work is required.
If you don't need to do re-work (either your part is cheap enough to scrap in case of defects, or your customer is willing to pay a premium for a compact product) then you reduce your courtyards dramatically compared to IPC recommendations.
On the other hand if you follow IPC recommendations you can choose from a wide selection of assembly houses, including ones using quite dated pick and place machines, and expect to get high yields (and thus low overall costs).