With the revelation of Bonney being at the top of the hierarchy for the Kuma-bots, it leaves me wondering if a similar reveal is going to occur for the Seraphim. However, I think the Seraphim might actually hold the keys to awaken themselves, rather than another Bonney-esque reveal. Allow me to present my evidence and explain my logic. (TL;DR at the bottom)
What we know:
Vegapunk clearly stated this chapter that his intention with putting Bonney on top was to ensure her dad will never betray her, and so he programmed all of Kuma's clones to obey her above anyone else. The Seraphim (minus S-Bear of course) are very clearly not in-line with that statement, thus it can be reasonably assumed that Bonney does not have authority over them.
The Seraphim have thus far obeyed all orders given to them by the person with the pre-established highest authority in a given situation. With one exception: Luffy was able to convince S-Snake to essentially disobey her given orders. This is most likely due to the real Hancock's infatuation with Luffy which was inherited by her clone because of the lineage factor.
We know that Stussy is the first successful cloning experiment, and that she has a will entirely of her own, with nobody outside of Vegapunk even being keen to her true nature. Vegapunk has repeated multiple times that she is her own person and he does not differentiate her humanity from "real" people. Similarly, the 6 paths of Punk all have their own agency and personalities, and they are even capable of betraying their creator. All of this is to say: every clone Vegapunk has made (that isn't a Kuma-bot) has their own will and ability to act freely.
This brings us to the Seraphim:
One could argue that due to their classification as Pacifista, they simply obey the chain of command. But given everything we've learned about Vegapunk, I refuse to believe he'd simply hand over weapons of mass destruction to the faction that he has been secretly working against since (presumably) Ohara. Vegapunk believes in the humanity of his creations, he doesn't see them as weapons, he sees them as individuals that hold the power to change the world for the better. To add to that, each Seraphim has shown varying signs of the personality of the individual they are cloned after.
Thus, I think it would be incredibly fitting for the Seraphim to be the ones that break their own constraints and gain their own agency. They obey commands currently because they're still basically infantile and don't know better yet. However, I'm betting in the future there will be moments where their lineage factor responds so strongly that they start to behave more like their originals and that will be what allows them to break free of the command structure.
S-Snake's infatuation with Luffy was the first breadcrumb, but as she is put in more situations that the real Hancock would respond to, that side of her will eventually surpass the "follow orders" nature of the Pacifista. It may take some time yet for this to fully develop, as right now I think most of the Seraphim probably start the final war on the side of the WG to heighten stakes, since their introduction as the replacement military power for the Shichibukai would be pointless if they don't act as such at least for a while.
I don't want to speculate too closely on what could cause them to "awaken" since most of this is already conjecture, but if it turns out this way I wouldn't be surprised if certain Seraphim remain somewhat antagonistic due to their inherited natures (looking at you S-Flamingo).
TL;DR
The Seraphim will awaken their own egos inherited from their respective lineage factor, and by the time all's said and done they will be acting with complete autonomy just like Stussy.
