The rule has to expressly say that it improves a FNP save or adds one to the roll. For instance, The Flesh is Weak rule that the Iron Hands has specifically says that it grants FNP 6+, and that if the model has FNP from another source, the roll is improved by one. So if you roll a 4, it is counted as a 5 when they have a Narthecium in the squad, which would make it successful and the 6+ version is simply ignored completely.
With your specific question, the Narthecium grants the FNP special rule. Death Company already have the rule naturally so one is simply ignored. There is no stacking and you just choose which FNP you are using.