Despite the similarity in appearance, the homunculus father and Hohenheim are not the same person. Though it is clear that there must be some connection between them. Though him not knowing Ed & Al were the Elric brothers makes that clear. While Ed & Al don’t need to use a transmutation circle for alchemy, Father doesn’t even need to move his hands to use it. To even add to the point, he is able to cancel the ability for the brothers to be able to use alchemy.
Interestingly enough, that doesn’t seem to affect either Scar or Mei. The fact that this catches Father by surprise is quite notable. It is clear that he looks at humans as beneath him, and it is just a matter of if they will be useful to him. The interesting part is turning Lin into Greed. Though, as Ed sees, he doesn’t fully change into Greed, as there are subtle things about his character that remain. Could they be cooperating, perhaps? This also brings up the question of Bradley because if Lin’s will remains, then you might have to consider Bradley partially human as well.
Well, it’s not a surprise that the homunculi have Roy and the Elric Brothers in a check situation. As long as they don’t get in the way of Father’s plans, they have no problem letting them move around. Though the threat is real when you consider the leverage of Winry against Ed. Still, this won’t stop Ed from trying to get Al’s body back, which they are close to. One odd thing at the end of the volume is the alchemist circle tattoo on the back of Hawkeye. That is quite interesting as to why she has that.