My understanding is you have two very isolated systems/circuits. One uses fuel, air, and a little electricity (glowplug) to heat the inside chamber producing a "toxic" gas byproduct (CO) that must be exhausted outside. The other circuit passes fresh/cool air over the heatsink fins of the chamber resulting in fresh/warm air being pushed out ot the "clean" output.
I think the most important point of keeping the intake for the "clean" and the "toxic" circuits separate/isolated is if there are ever failures in flow (e.g. a blocked or kinked exhaust, or other malfunction) that it is less likely to result in toxins being pumped out or leaking out of the intake end and into your living quarters. I have a limited understanding of these systems and have only been using them for a few years now, but this is what I have gathered.
I once thought of experimenting with improving efficiency by twisting the intake and exhaust tubes together, effectively transfering heat from the exhaust tube to the intake tube to pre-heat the intake air. It could be improved by also covering the twisted pair of tubes with a suitable insulating covering. The intake tube would then be extended and located away from the exhaust to prevent it from drawing in exhaust
I never got around to experimenting with this idea because these diesel heaters are so effective, I don't think the effort would really pay off. My heater is so effective at lowest settings that it feels like it's overkill. Mine is one of the pricier Planar-brand heaters, but from what I hear the Chinese ones are just about as effective and a much better value.
My 2cents
P.S. if my Planar ever dies, I won't be forking out another $800 for a new Planar, Webasto, etc. I'll instead be buying two cheap ones for ~$300, keeping one for parts if ever needed.