I've seen it done before the way you describe and didn't care for it.Besides taking away from precious space from the display,the section partitioned isn't nowhere near big enough for proper function.A sump should have as much area/water volume as possible.The more water in the system,the more the system will be stable.With 12" of space,it will be very hard to make a proper skimmer section with a constant water level and a slow raw water feed.Then you'll still need room for a return pump and float valve/switch.You will also not be able to upgrade your sump to incorporate a fuge.I understand your fears of drilling/plumbing an under tank sump but when done properly,there's not much to worry about.If you need pics,check out my 40gal project log thread.Another concern you might have is drilling the bottom of the tank for an overflow,these types of overflows are no where near as efficient as a horizontal overflow along the back glass.They are drilled up high just inches under the water level.If anything were to ever happen,the tank would only drain a couple inches although i've never heard of anyones failing.They also provide much more linear inches of overflow -vs- the corner overflows(40"-48" compared to 12").This will allow a very thin layer of water to be skimmed from the surface which is much more efficient at getting these surface trapped organics to the skimmer as well as quieter than corner overflows.
The benefits of a long(at least 3',i use an old 30gal tank)sump far outweigh the convenience of a small in tank sump IME.With 3' of length,you will be able to partition it(glass can be cut to size at HD if you use a tank) easily to make a proper skimmer section with a constant water level and a raw water feed from the output of the overflow.You will be able to make a large fuge,design proper baffles to get rid of microbubbles.Float valves/switches are easily to corporate into the return pump section.As well as increase the total water volume of the system as much as you'd like