Don't imply inferior with surface mounted components. I only noted that the size do affect physical parameters. In some situations it is better with hole mounted components. In some it is better with surface mounted ones.

When you have solder joints, the solder material is behaving similar to a very high viscosity liquid. If you put a force on the solder joint for a long time, you will be able to move the component. Because of this, you do not want heavy surface mounted components on the botton of a PCB. And you normally prefer hole mounted connectors, so that the pins will act as mechanical stress relief if there is weight on the connected cables.

The small dimensions of surface mounted components is not only an advantage in giving you smaller equipment. Being able to shrink the physical size, will also allow you to better shield other parts of the electronic from noise. And the lack of holes in the PCB means that you can have a solid ground plane in the PCB.

A surface mouunted IC has the same silicon chip inside as a hole mounted IC. For most IC, the performance will be identical. But for some buffer chips, the maximum output power may be lower for the surface mounted chip because the smaller outline doesn't allow the same amount of power to be radiated from the chip without a higher chip temperature. In some situations, this can be mitigated by using the PCB as heatsink. Sometimes that isn't enough.

When ordering a PCB, you can buy small or large series - it doesn't matter if the PCB is intended for surface mounting or hole mounting. If you want your components mounted, there are companies that specializes in building prototypes and small series products. If you intend to solder the components yourself, it is way easier with hole mounted components. But with a steady hand, good eyes (or a special stereo microscope) and the correct solder tools, you will be able to solder most surface-mounted components too. The main exception is components using BGA (Ball Grid Array) or similar, where the solder joints are under the component instead of around the sides. These kind of components are intended to be "baked" - you heat the PCB and components until everything gets hot enough that the solder paste melts, and for that you need a factory with a suitable solder oven.

Transistors and some IC that have special pads for cooling can normally be soldered by hand. The big problem is components that have a big solder pad under their belly. But you can often avoid that kind of components. They are power components, and might be a switch regulator in a DC/DC power supply, or a current regulator for a USB host port or similar.

There are huge amounts of standard boxes available for just about everything. The biggest reason for custom boxes is normally not that you can't find a suitable box, but that you want your product to have a special graphic design. A company having multiple products normally have a profile, and you strive to make the products look similar.

Most companies do test their equipment in stressful situations, to make sure that the warranty costs will not sky rocket because of a bad design. In some situations - for example vehicle use - there may exist explicit regulations that the unit must pass. If designing for vehicle use, you will have to select automotive-classified (or better) components, that are classified for extended temperature range. And the product will be tested with high vibration loads and with strong shock tests, to make sure that you don't get mechanical or electrical failures. For vehicle use, you will normally also test that the unit works correctly (or - if allowed - recover correctly after a crank test, where the supply voltage gets very low for tenths of seconds. For general-purpose equipment, it is normally enough to prove that the device is safe and that it doesn't radiate too much noise. But special equipment such as fire alarms or similar, you will have to research what additional certifications that the device must pass.

There are several steps in factory testing. The PCB is normally electrically tested, to make sure that pads that should have contact have contact and that neighbour traces does not make contact. After the components has been mounted, you often use a bed of nails, where a large number of sharp needles gets pressed to test points (often extra pads on the PCB) and critical voltages, pulse forms, frequencies, ... are measured. For a processor-controlled product, you normally run a test program in the processor, where the processor toggles all accessible signals while external equipment verifies that the signals do toggle, or power is turned on/off to board sub-systems etc. The PCB (together with non-soldered modules) are then fitted into the case and all internal connectors are connected. Then a final test is performed, where you connect external cables to all connectors and do a functional test of the full product. Depending on the complexity of the product this may be a very simple "it works" test, or the product may be put through a large series of tests - sometimes fully automatic, and sometimes by a person. For simpler products, the end result of the testing may be pass/fail. For more complex products, the factory may log a number of measurements for each produced unit, to allow statistical analysis.