I would like to have a floor made of wood that is as warm and natural as possible, because it is breathable.
I’m not quite sure what is meant by breathable here. Wood can absorb and release some moisture, but only for buffering; you still have to ventilate yourself. A wooden floor is warm mainly when it is well insulated against the ground. Without proper insulation and sealing, it can be cold and drafty – but in new buildings that is less of a risk.
Wooden floorboards. Maybe even spruce/fir.
Wood is not a good heat conductor. For floorboards, I would make sure not to choose too thick a thickness, rather around 20 mm. Spruce/fir/pine are often thicker because they are less hard and also poorer heat conductors than, for example, oak.
Compared to a floor heating system embedded in screed with tiles on top, the flow temperature probably has to be raised a bit (!), so in combination with a heat pump, floorboards are not optimal, but with a gas heating system, it’s no problem.
But how do you construct something like that in combination with underfloor heating?
Not much different than without. Substructure with insulating mats in the gaps, just not flush with the upper edge, but slightly below. Above that, in the remaining gap, lay the heating pipes not in a coil shape, but in straight runs back and forth (supply and return side by side), and notch out the beams of the substructure at the transition points to the next gap. Use metal plates for better heat distribution. There are ready-made systems for this; sometimes special insulation mats are specified, but usually natural ones based on wood fiber or other natural materials. The search engine is your friend.
That doesn’t work. Period.
If you have absolutely no ... no ... I’ll restrain myself from commenting. Just this much: Yes, it does! Period.