Every single of your questions depend on which components you place, carrying which current, being exposed to which voltages, at which frequencies, and being near which signals being used by which circuitry.
Sure, there's limits on how accurately a pick and place machine can work. These are rarely the limits of how closely you pack components.
So, no, you don't talk to the EMS all the time when designing a board – you talk to yourself (or colleagues) and figure out what the physical limits on placement actually are – that might be
- geometry dictated by the fact that you're not placing components on the board for fun, but to fulfill a specific purpose. For example, a 90Ω differential microstrip line has a specific distance between the two conductors. When you add AC coupling capacitors to these lines, it's not the components that limit your spacing - it's the physics of transmission lines.
- creepage distances or clearances due to high voltage needing to be handled safely (and what these are depends on the voltages, the operating conditions, the safety requirements and the targeted reliability)
- signal integrity considerations: place a high \$\frac{\mathrm d}{\mathrm dt} i(t)\$ line of your SMPS parallel and close to your sensitive analog signal line for long enough, and you've built a transformer for noise coming from the former to the latter. That of course also works with power inductors and signal capacitors, for example.
- thermal considerations might say that your resistor can be cooled well enough through the board if there's not too much heat dissipated by surrounding components. You can't thus put it close to your power transistor, but very close to your other transistor that doesn't dissipate much power in your application
These couple of examples serve to illustrate that you need to understand what you are making a component do, and only from that can derive distance bounds.