The translation of Griffith's panel makes me wonder: are the boy's feelings intertwining with Griffith's psyche the ones that make him (Griffith) feel that sense of desolation (maybe incompleteness?) after achieving his dream (if he's talking about his Dream -the castle- and not about his sleep)? Or is it that Griffith wasn't able (or didn't want) to sacrifice all of his humanity during the Eclipse (same as the slug baron... Although Femto is a member of the Godhand and Slug is just a 'mere' apostle...), and thinking some steps forward in the chess game, he planned on taking over Guts and Casca's baby so he could be with them sometimes, without harming them, because of his human regret towards his sacrifice?
There's a lot to unpack in what you said. First off, people don't sacrifice their humanity. They tend to offer other people as sacrifices in exchange for evil power. What happened with the count (not a baron) is that he sacrificed his wife, but still had a daughter, and despite having become a monster, he still loved her. So he was conflicted when it came to her, and in the end he couldn't get himself to offer her as a sacrifice too. It's a very specific circumstance, and it doesn't diminish the fact he was an evil monster through and through.
Now about Femto. He has different circumstances, and he is indeed a member of the God Hand, not a mere apostle. He has made it clear before that he, as Femto, has no feelings whatsoever towards Guts and Casca. However, we saw in volume 22 that the boy whose body he stole when he was incarnated hadn't been destroyed in the process. Somehow his consciousness survived the takeover of his body. That consciousness was awakened when he felt that his parents were in danger, and he even managed to compel Griffith to move to protect his mother.
Afterwards, we saw that during nights where the moon is full, he was able to revert his body back to its true form (reshaped within the beherit apostle, from a misshapen baby to a 'normal' boy). He did so whenever his parents needed him. The question that's been lingering this whole time is something you hinted at: just how intertwined are the two of them? And that's really crucial for the end of the story, because as I mentioned many times in the past, it's likely to revolve around the conflicting goals of saving their son and destroying Griffith.
To put it more simply: can Femto be split from the body or are the two of them irremediably fused together? I think for all intents and purposes, there needs to be a way for the boy to be saved at the end, as I just don't believe Miura would write an ending where he doesn't survive. However it might be not immediately obvious and I feel like that unknown factor would be a great source of tension and drama from a storytelling perspective (possibly up to the very end of the story).
Finally, about what the words mean in this speech bubble. Given that we're missing at least half of what he says, it's better not to draw too many conclusions yet. It's possible he's just commenting (as Femto) on how he had these dreams, and that's how he realized the boy was taking over the body. That would put them as two firmly independent entities. It's also possible he's talking (as a mix of the boy and Femto?) about how visiting Guts and Casca and feeling that warmth has been nice, but the "dream" must end. And of course he could be making a parallel between his "dream" as a reference to his all-encompassing ambition, and the boy's overwhelming desire to be with his mom and dad. These possibilities aren't mutually exclusive. I'm even reminded of the beherit apostle's words to the child as he swallowed him:
"Taking the new world inside me as a cradle, dream."
What's for sure is that he's not talking about regrets he's having, as Femto, about his sacrifice of the Band of the Falcon. He doesn't have any. And I don't subscribe to the idea that, having barely been reborn as Femto, he hatched a plan that would lead to him being incarnated in the body of Guts and Casca's son. He raped her out of spite without any secret plans, and as far as we know sharing the body of their son isn't something that works to his advantage.
Maybe it's at this point in the story, when Griffith reveals himself to Guts and Casca as the Moonlight Boy, where SK's words («Your wish may not be her wish») incarnate in utter conflict.
Well it's like I said above. Beyond this specific scene, the issue is going to be the conflicting goals of saving their son and killing Femto. It's not hard to imagine that Guts would (initially at least) favor revenge while Casca would care above all about their son's well-being. This brings us back to the question of whether they can do both or not. The way I envision it is that, yes, they can actually save the boy and get rid of Femto, and eventually (after a good amount of character development) Guts would come around to the idea that saving his son is what's most important.
Let me share a mental image with you: At the end of the series, as he grits his teeth and swings the Dragon Slayer at Femto in Falconia, we see Guts' internal monologue as he thinks: "Not just for them (shot of the Falcons) or to save this world (shot of people, elves, whatever), but most of all, for him... (shot of his son)". Thus, completing his long character arc, from his introduction as a man drowning in darkness and on a path to self-destruction, to being himself again, to remembering his priorities, to finding new friends, and finally to his redemption as a man fighting out of love for his family rather than hatred for his enemies.