That's a bug.
If you play with futa content turned on, it's a futa game. If you don't, it's not. Also here's some explanations of why the characters have dicks (these are all based on having futa content turned on obviously):
Amy: She started out hating it, as everyone she told about it rejected her for it, except for Claire. But after meeting MC, she finally met someone that didn't reject her as a freak and actually embraced her and was sexually interested in her even though she had a dick. So now she's not sure if she really hates it, because it wasn't that she didn't enjoy using it, just didn't enjoy the rejection that came with it, but now she doesn't have to worry about that with the MC around. On top of that, she has the temporary cure, so when she wants to be female, she can be, but when she wants to enjoy having a cock, she can do that too. So right now, she's undecided on her future and a cure.
Meg: She's a demon that enjoys being intimidating and domineering in life. So obviously that spills over into her sex life. She enjoys power and having a cock makes her feel powerful. The fact she specifically chose and designed her own body and cock and gave herself a giant dick is entirely in line with her personality. That's without even going into the fact that so far we've only actually really interacted with it properly once and that was clearly spelled out as being only a reward for behaving herself and won't be a permanent thing.
Phoenix: This one is just entirely optional, you even have the choice to tell her to get rid of it before you interact with it. Although I did fuck up and forget to put a variable in there that tracks that choice, which I already added earlier today. Her reason for having one is stated in the scene you see it. She has a cum fetish and enjoys sucking her own dick. She also is an expert at manipulating her own body, so it's not really a surprise she would try giving herself a dick at some point and realise she enjoys it. Not only that, but she isn't a main character and won't be a huge focus.
Sam: Sam is the only true futa in the game, she has both a dick and a pussy, but we've only seen her once and she won't be a main character either, so won't really be a big part of the game. As for her reasons, we may find that out later.
So, take away the two side characters and you have 2/6 main characters that are futas and one of which isn't even going to be a futa every scene you see with her. So where exactly is the excess?
I don't want to spoil any of her story, but I will say if that's a worry, don't skip her content