As much as I like to play detective, there are 3 things that I hate touching. Deus, Gods and Shopkeep.
A small summary of clues on Shopkeep
1) He has at least 2 shops that he runs himself.
2) MC's memory powers don't work on him (and he also knows about them and exactly how MC uses them).
3) He can divine information like he does with the twins and he seems to be able to forsee events.
4) He has things that are out of this world, and he is well versed in them.
5) He seemingly has a supernatural power relating to deals and breaking a deal with him may cause instant death.
6) According to him he isn't a superhuman or a monster.
7) His and Charlie's powers sound similar so he probably has the ability to infect or grand powers in some other way.
So what do we have that fits the bill but isn't a superhuman or a monster?
These are the entities mentioned in the game:
Human / Humans don't have powers, so this one is out.
Althuman / Possibly, although doesn't sound like the ones from the memories.
Superhuman / He claims to not be one. Although he would be a Superalthuman if such a thing makes sense.
Monster / He claims not to be one.
Apostle / Possible? but very uncharacteristic behavior.
Arbiter / Highly unlikely.
Undines / Don't exactly know what they are but they sound like monster factions to me.
Strength Eaters / Same as undines.
Gods (Great Sea, Lord of the Dark, Outer Twins) / Possible, Aglaecwif says that only Outer Twins are true gods, so the others could just be very powerful beings that are neither true gods, nor monsters.
FIltering out the possibles list for clarity from more likely to less likely:
God (of the lesser kind)
Althuman / Superalthuman
Apostle
Lastly, another option which has a lot of merit:
Aglaecwif said:
Female "I'd have it in my hand already, but the fiend who gave it to you seems to have decided I can't take it without your permission."
This could be angry talk, or fiends could actually be a type of beings, not unlike what we consider devils/demons and the like.
So to summarize:
I think he is either a lesser god or a fiend but I leave open the possibility that he is an Apostle avatar or an althuman "spawn" that is uncharacteristically strong.
I won't bother going further into it. There just isn't enough info available.