So I read your fluff and picked up these key points:
-Loyal to the Emperor rather than a Primarch
-Estever-specializes in hit-and-run tactics
-Athaem-reliable, well trained
I'm not really sure what their specialty is as a chapter though. Maybe you could elaborate. That would help with developing rules. As for the comments below, they are blunt for the sake of simplicity, not rude-ness.
He should be S4, W3, and A4. Nothing about his fluff indicates he's a super marine
I would drop Fleshbane. That tends to indicate more of a Poison and since Shread already lets you re-roll failed to wound, its a bit redundant. I would make it AP3 though.
Nimravidae looks fine.
Drop Fear, Rampage, Counter Attack, and It will not die. He's a hit and run specialist. The above rules don't really represent that. I would give him...wait for it...hit and run!
I would give him Infiltrate and Move Through Cover.
Company Tactics. Again the Rampage thing doesn't make much sense. This one is hard to nail down without knowing the 'style' of your chapter.
Master's Chosen. Drop Rage and Counter attack. I would say something like, Estever typically deploys with a squad of his most chosen warriors. These warriors are equipped with only the best weapons from the Panther armory. The unit that Estever is deployed with (note: not joined) gains +1WS as well as the Shred special rule to represent their powerful weapons.
Points after edits: 210
Points as you have him: 300+
Statline: Looks fine
Staff of Sight. The Mastery Level and knowing 4 powers is pushing it (think Ahriman) but ok maybe he's trained so long and that's why. I would keep it AP4 like the power maul in the BRB though.
Armor of Truth. Fine
Living Ancient- Way OP and doesn't make much sense. Why do they have Feel no Pain? Why are they all psykers with force weapons and why can they all cast psychic powers when no other squad of psykers in the game can do that? Also why are they no more expensive than a normal tac squad?! I would change this rule completely (I know you said not to, but it makes no sense to me). Since he is the most reliable Librarian ever, I would make this rule something like, Athaem has been studying the psyker arts for far longer than any Librarian in the Panther Chapter. He may reroll a single psychic test once per game, but must keep the results of the second roll. It's not nearly as powerful a rule as your original, but remember, he's only 185 points which pretty much covers the ML 3 and not much more.
Company Tactics. I also don't get this. He's a combat Librarian, why's he redeploying units? Again, hard to work this rule without a Chapter overview.
Psychic Powers: Sure.
Points after edit: 185
Points as you have him: 285+
Your fluff indicates that he's a siege specialist, but your rules indicate that he's a combat beast along the lines of a World Eater. I'm going to tweak according to the siege specialist aspect.
Statline: I think you know what's coming here. WS5 BS5 S4 T4 W3 I5 A3 Ld10
The Beheader. Not a fan. Again it sounds more of a combat specialist thing. I picture most Siege guys with a big hammer. I would give him a Thunder hammer. It also goes nicely with his storm shield
You could give it armorbane though to represent its ability to tear down walls and what not.
Terminator Assault. No. It's way too good. Not many armies are equipped to deal with mass terminators deep striking normally. How are they going to handle half of the units DSing turn 1 automatically
? There's a reason terminators aren't allowed in drop pods. It's also not related whatsoever to being a siege specialist. I would drop this rule completely and come up with something new.
Perhaps, something like Isdan and any unit he has joined add +1 to the damage table when shooting or attacking buildings. They also gain Move Through Cover (Ruins)
In addition, Isdan is an expert at picking out the weaknesses in enemy fortifications. He may reduce the cover save of one building or fortification on the battlefield by 1 points. So an Aegis defense line would be reduced from a 4+ cover save to a 5+ cover save (3+ for going to ground).
Heir Apparent. Not sure what this does.
Bionicized. It's fine.
Points after edits: 175
Points as you have him: 300+