Main reason not to have the raft tanks and fish tanks combined has to do with the solids building up on the roots and impeding oxygen exchange for the roots with the water.
Also, makes it hard to see the fish and feed the fish without disturbing the plants.
The raft tanks don't need to be especially deep while the fish do a bit better with deeper tanks. Having the added water volume of the raft tanks does improve the system stability an improve quality for the fish even if the fish don't have physical access to the space where that extra water is.
First: all the numbers and calculations necessary to design your system are available, but they are scattered all over the Internet. During my study I have tried to assemble them in an Excel sheet. I enclose the sheet, but use at your own risk and read the papers that led to the calculators, it will give you lots of insight.
As for design, I am under the impression that a lot of possibilities are overlooked and older systems are forgotten.
Existing systems seem to be considered as end of design.
I like to think out of the box. That is the subject of this thread.
I aim for energy conservation and simplification. To reach that, I am not afraid to first think complicated, then I keep the good parts and try to simplify.
Let me fire my ideas on you and please comment.
30 years ago, I had a big aquarium with a bottom (under gravel) filter. A pump circulated the water. I don't remember the filter ever clogging, but I might have forgotten.
that thought raised the questions:
1. why is it that in raft aquaponics fish are not grown under the rafts?
After all, there is where lies the biggest water body in the system.
Or in between rows of rafts, i.e. in long cages? This would keep the fish away from plant roots if that forms a problem, and make harvesting easy.
Fish densities overall would be much lower.
Even if the gravel would tend to clog, there are vacuum systems that allow the gravel to be cleaned, either directly in the water, or outside, in a filter system.
or an array of drainage pipes would allow to pump out most of the solids, (settling and floating) to a filter
2. rafts are used because they float, but the problem with them is they cover the water surface and impede oxygen exchange, this on the largest exchange surface in the system.
result: much more aeration needed, much higher energy consumption.
Easy to solve by using floats and grating to support the plants.
3. another problem with rafts is plant roots permanently in the water. It is one of the advantages of ebb and flow in grow beds
Solution: use hollow floats that keep the plants just above water level, i.e. standing on longintudinal racks.
These racks can serve as separation of the rows and form the sides of the long cages.
at regular intervals, pump air in the floats, the roots are lifted out of the water, are thoroughly aerated.
let the air escape, the roots are lowered and in turn aerate the water.
Ebb and flow turned upside down. Perfectly adjustable to different plant needs and stadia.
Cheapest would be long inflatable tubes.
hollow bottomed floats with solid sides would favourise oxygen exchange as the pressure on the air increases.
extra advantage of this system: a square tank is cheaper to build than a long narrow one
that's about it, for now