Theory: If Luffy's group found the real Vegapunk, presumably it's in the junkyard. What if the satellites rebelled against him or otherwise got out of control? They could have made the Seraphims against his will, and he's hiding out in the junkyard till the revolutionaries come to save him. It'd explain why he's good but also works for the WG, why Oda split the SHs up, why Lilith is untrustworthy, and to get into the "evil science" of cloning and genetic engineering etc.