Jubei got Sekigan from Rachel or Clavis Alucard, Phase Shift 0 tells that his eye was destroyed after fighting the Black Beast Remains.
Jubei probably knows of the time loops via Sekigan which explains why he didn't recognized Bloodedge.
Jubei wouldn't let the time loops occur because that meant the rebirth of the Black Beast
Therefore, Jubei is Not the owner of Amaterasu.
Amaterasu made the time loops.
Takamagahara (Yes it's spelled like that) just observed them and searched for a way to inherit the azure so it could have the same powers of Amaterasu.