Fiducials are used by the pick and place machine to provide better accuracy when placing components on the PCB. There is a camera that recognizes the fiducials and uses it as a registration point to calibrate where the machine thinks it is on the PCB.
There are two types of fiducials: Global and Local.
Normally a PCB will have 3 global fiducials per side (top & bottom), and usually in the corners of the PCB. This is so it can recognize the boards overall orientation and position.
Local fiducials are located near some of the critical parts. Usually there are two fiducials for each part, in opposite corners. IF you have several critical parts that are close together then a fiducial can be shared by two or more parts-- reducing the number of fiducials required and the the PCB space taken up by them.
Where you need local fiducials really depends on the pick and place machine that will be used, and the placement accuracy required by the component. Chips with a finer pin pitch will need fiducials more.
It's interesting to note that TQFP's need fiducials more than most BGA's. Most TQFP's have a pin pitch of around 0.5mm, while most BGA's are 0.8 to 1.27mm. BGA's also have a cool ability to somewhat self-align due to the surface tension of the melted solder. But I need to stress that this is very component and machine dependent, so check with your assembly shop.
Also machine dependent is going to be the construction of the fiducial. Things like how big the pad is, and how much the soldermask is pulled back. Usually the fiducial is round, but sometimes square or bow-tie shaped.
Another thing is that some assembly shops will request fiducials to just feel good about things-- but don't really need them. My second to last PCB had had lots of fine pitch BGA's, QFN's, and TQFP's and had no fiducials on it, but there were no issues with parts placement. My current board is nowhere near as difficult but they are requesting fiducials. Go figure. I'll humor them and put the fiducials on it.
You can fake this pretty effectively in Altium Designer.
Altium has what they term "Recyclable Schematics" - Schematic layouts that you can paste into larger schematics and treat as components.
Duplicating the PCB end is a bit more work, but definitely doable (I've done it). Basically, you route the DC-DC on one board, and then simply copy-and-paste the design into whatever new board you have. This will move the component footprints, and traces, but not the nets. Then, assuming you have the corresponding schematic entity, the next time you synchronize the schematic and PCB, Altium will match the free-floating footprints to their schematic entities, and add the netlabels to the existing copper.
Alternatively, assuming you are OK with not being able to edit the DC-DC layout in situ (on the PCB), you can just paste the layout into a footprint library, and define where you want input and outputs to be.
In this case, you would edit the library file, and then propagate the changes out with the "Update from PCB libraries". You can also modify the primitives of a component once it has been placed, but changes there will not propagate back to other places you have the component.
Third, Altium can embed one board into another - I use it for panelizing things, but I think you could probably also use it for embedding one functional section into another. It wouldn't tie into the schematic, though.
It's worth noting that I do the first two of these regularly at my job (usually with FTDI USB-Interface circuitry) - It's definitely a viable approach.
Best Answer
Extra/omitted parts on a PCB can be very useful for
a) Having multiple versions of a circuit able to be built with only one PCB
b) Debugging, when I lay out an RF board I often put an omitted 1k SMD resistor from the line finishing near to a ground pad. Invaluable to solder a 50ohm coax to for probing the signal on the line, with good RF integrity and without damaging the line. A JTAG or RJ45 socket may be handy for digital access to a board for debug, but is not needed in production, it's omitted for cost or because it won't fit in the final production case.
c) You may often see a 0 ohm resistor in series with a power line, for monitoring current, or isolating parts of the circuit. These pads may also have a trace under them to short them in the normal case, the trace can be cut to use the component.