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.
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.
Best Answer
I have been designing some PCBs recently and I would suggest you NOT to use auto-placer or auto-router for your final product. (Proteus has auto placer.)
First of all - Your software is as intelligent as an earthworm when it comes to auto placement or auto routing. In other words, it's dumb as a potato.
Auto routing would not know which placement will get you a better trace pattern which will enable you not only to make an efficient design but also to minimize noise in the circuit. Similarly auto routing doesn't know that shifting a component slightly to the left or right would enable you to route a track in a better way. These tools will just give you a design which is correct according to the circuit. But when it comes to real world performance, things are different.
For example:
Your software won't respect these concepts because these are not mentioned in your schematic. You will know only when you have got the PCB manufactured and it doesn't work as expected all the time. I am not saying it won't work. It might work, for 90% of times but you have to take that 10% into consideration too.
My suggestions is that you should learn some PCB designing concepts and try placing and routing on your own. You can always post your schematic and board layout in forums and experts will give you their opinion/suggestions.