Hello!! interesting thoughts! while ı lack some game content on my mind ı will try my best to share my thoughts with things ı remember well ^^!!
spoilers of main story:
İn the main story ıts admitted that MC's ashes are taken by the İsaac's ancestors because regardless of MC was involved with devil or not they had some sort of power and ı guess when you are in era that things sound pretty hopeless this noble family thought swooping some ashes and hiding them wont hurt. But honestly ıt could be related to Jonas (also the voice) interfering in this matter beforehand since we know he can speak to others thorough their dreams too (he tells the ancestor of Isaac that ıf they secure the ashes well he will grant them a chance of immortality + powers thorough some risky ritual). But ım not so sure ıf Nathaniel was in this scenario yet because in the Allele wiki the ages (written by the game dev herself) tells us that Nathaniel was born in 444 AP and İsaac in 509 AP and in the library of blessed family members (Ashborn members) there is quite a list before ıt comes down to İsaac plus the first member becomes born around 10 AP gets blessed (and becomes firt blessed mother) and stays in the position until 298 AP years. so ı think Nathaniel was not included in the process of securing the ashes but for some reason he has red eyes as ıf he took the ritual and got blessed by himself yet you cant see his name in the lineage book.
For this matter ı believe he is a special case and perhaps joined the house around third or fourth heir (ı would also love to add that this ritual is special for ashborn lineage ıf ım not wrong which makes Nathaniel extra special due to his name not being even in the lineage book). Regardless being a butler even ıf he wasnt involved in the process of securing the ashes from the start HE DOES now proctect them and make sure that ashes never run out. By saying that ı mean in rituals whoever will take the ritual has to drink the special drink made from the skull that has been grown off the ashes. Nathaniel makes sure by salvaging any ashes during the rituals so ashes wont run out by the growing bones from the ashes (ıdk how he does that honestly this is extra Q/A ı had in the past with game dev in the past and ı kind of forgot the details but ı suppose he is salvaging them from leftover crushed bone ashes during the preperation of drink).
As for the theory of him doing the first ritual. ıf my memory of only ashborn family can take the ritual is true (which is highly the chance because ıf everyone could take it why the married spouses of the family members didnt take it at all?) then ı doubt he gained his powers thorough the same ritual ashborn family did. or even ıf he did gain that power like ashborn family -thorough the ritual- his circumstances are alot different than them ı think.
VERY MAJOR SPOİLERS FOR THE MAİN GAME: (these spoilers are from my Q/A questions with game dev and they could be altered & changed as the game goes on since ıts more like planned future of of Nathaniel in Allele story PLUS this text wall HEAVİLY includes my theories and thoughts so while ı believe ım close to the story of the game ı cant tell how much and would like to take everything ı said with grain of salt regardless. this sections is written for cool game debating than just game info giving ^^ )
As for him acting like they are close yet him acting bitter. Lets say that there is a special link between Nathaniel and Jonas and your theory is actually partly true ^^. Jonas did wanted to be with MC but he decided not to interfere the matters by himself existing in the world since he is... well much more stronger being than normal human and his original existance could change things but Jonas wanted MC to experience things without major change so instead him showing up the world he preferred to stay back and appear in MC's dreams while sending a ''part'' of himself to the world to possibly guide the MC thorough the better end while keep letting them to experience the world by themselves. This is exactly what Nathaniel is... the guide of Jonas yet he is a person himself too so technically he is a fragment of Jonas who lived as ''human'' in his entire life and is not aware of Jonas's existance... well by the spoilers of the card game we should say ıts more like he is aware by the time of the side game appears but he seems to be staying in denial because ıts such a major change for him. İmagine living years upon years of what you think that is your life and then you learn that your life was infact nothing but a small piece of much stronger and greater being and once the time ends.. you will go back to this greater being as you are nothing but a mere piece of them. I think Nathaniel more like wishes to live his remaining time with the things he usually did and lived rather than ponder over it though because whatever he will thinks or feels wont change anything. Plus like said Nathaniel is technically a human since Jonas only created him as his piece but never interfiered with his life either. Sure he is strong since even as a fragment he belongs to greater being afterall but his thoughts, acts, emotions are still very human and not only the memories of the Jonas's is overwhelming but also ıt affects and alters his own thoughts and emotions that he honed by himself and he doesnt want this change. For example; Jonas does care about MC alot but his love and care is currently more like platonic since between MC and Jonas there isnt any power balance as MC being a human. But for Nathaniel this case is bit more different he is a human too afterall and he is compared to Jonas.. very immature. Jonas can tell any kind of close relationship with no balance will lead up to disaster and can alter his emotions according to that. Nathaniel in the other hand cant because he lacks the very knowledge and maturity to do exactly same as Jonas yet ı feel like he can sense that such relationship would not end good either which is my theory. Nathaniel can sense being close to MC wont do him any good yet he cant control his emotions and thoughts like Jonas do so he has so very few choices: stay away from MC and dont let them get near to him or accept the doomed fate by being defeated by his emotions.
Anyway these are what ı think ^^ ı am curious of what do you think!!