If it’s any help… I also didn’t understand your observation, not clear on the considerations from an automotive engineering point of view (this not being my field).
From an engineering perspective, you'd put the unit where it belongs, in the electrics compartment and you'd keep the wiring as short as possible. On modern vehicles, you'd often see a setup, where additional control units are sitting right atop one of the batteries. A good spot. Where it sits now, that was probably the only sensible place in the vehicle above wading depth, that could accommodate the rig, after the principle layout of the electrics had been already decided upon. Heat is another issue, the area is not well ventilated, if at all, plus, heat is being emitted from whatever sits underneath (gearbox..?)
Also, you might want to see the control led´s, to check for proper operation, how does that work ?
On another note, the + connectors ought to be isolated and shrink tube being used at the ends (the red bits.?). Normally, you do not see any surplus cables tied up on a new vehicle, but the wiring is routed, protected and secured properly...none of all that here.
Speaking of which: the owners wishing to keep the IG forever might want to look at sealing all the resident electric connectors with wax. Why ? After about 15-20. years of operation, you'll find electrical faults appearing, without any apparent reason. On French built vehicles after just 8 or 10 years, traditionally. The phenomena is caused by oxidation on the positive and corrosion on the negative. Everyone who has worked on vintage cars will be familiar with it (swap + and - on pre ´6x UK vehicles)
Porsche and Mercedes do not suffer from that syndrome, from what I know, the only two manufacturers using a silver coating on contacts. Main problem is obviously the negative circuit, not the positive, although both suffer over time.
With all due respect to the massive engineering task, the wiring of that CTEK looks more like from a model railway than a tough utility vehicle. The CTEK itself is totally unsuitable in my book for durability off-road, as mentioned before...
