You often prototype with hole-mounted components. Either on bread board or by drilling holes in PCB and soldering.

For real products, you instead use surface-mounted components. The components are very small compared to the hole mounted versions. But while reducing the size, their capabilities are also reduced. When making resistors smaller, they will support less power before overheating, so you must check the power for each used resistor. When making capacitors smaller, they support less voltage. A number of transistors and IC will have special pads that must be soldered to the PCB for using the PCB as a heatsink.

If not using a standard casing, you ask a designer to use CAD software to create blueprints for a new case. The designer can normally supply you with a 3D rendering of the box, so you can view it from different directions and in different colors and decide if you like the look. You then contact a plactic factory to design the tools for making the box based on the blueprints.

The distance between adapter and electronics is normally not too important. But all signals leaving the PCB, and a lot of signals inside the PCB should be protected. For external signals, you may need to clamp overvoltages. And you may use EMI filters to block noise - normally from going out from your electronics, but in some situations to filter away external noise. For internal signals, you will often have to add series resistors to reduce the noise. The series resistor will slow down the flanks of the signals when a signal change requires charing/discharging of the capacitances in the circuit. For the power supply, you may have to add chokes to filter the signal. And you will need capacitors between Vcc and GND close to most IC.

Not sure what you mean about testing. Depending on what product you make, you may have to send a unit to a test institute, to have then look at the design and measure emitted noise etc before giving you a certificate. For production, you will have to design test equipment that will automatically test all critical parameters of the product, so you can find if there are bad solder joints, solder connecting two nearby pads, a missing component etc.

To produce a commercial grade product, you will need knowledge in a lot of different areas, or you will need to use a consultant to make the design and get the product through testing and prepare the required production and test documents.