if you really want to go small you can build your own gold wire bonding machine, a bit like a 3-d printer but uses fine gold wire and pressure (via a knife edge), the company I once worked at made one, but you do need a clean room and a supply of the bare chips (no resin package so just bare silicon die) then you simply wire bond multiple dies onto a very small PCB probably made from alumina ceramic.....
OK if your making many, but probably 100's rather than 1000's actually once you have the kit :)
seriously what you could try is rather than have a single PCB, use multiple smaller PCBs that are then stacked on top of each other, a bit like the arduino shield type of idea, but much smaller. You'd probably need to go BGA (ball grid array) package so another level of soldering as you have to use an oven (or hot air) rather than a soldering iron. You'd end up with more of a cube, but it would probably make better use of the available volume but heat transfer is a pig so put the high power devices on the outside....
Actually, thinking out loud, if you put all your electronics on a flexible PCB (more common nowadays) you could simply roll it up and push into the WTC .... sorted.
As mentioned, with high enough volumes you can get the chip functionality you need and no more, in the smallest package and use the latest manufacturing techniques not available to us. You don;t need to have the latest stuff yourself now, you use a contract manufacturer who has and can spread the cost and knwos how to use it.