I don’t know about the rest but I think he didn’t try to take her because he knew she wouldn’t want her child to grow up with a yakuza or because she knew that the seme and uke would take care of her even though they aren’t the real parents. And she probably already guessed that they had feelings for each other or that the uke had one sided feelings for the seme ┑( ̄Д  ̄)┍
Her being able to rely on sentarou for this doesnt really mean that he is the dad though.(And if it was really sentarou, i feel ljke she could have told him before)
BUT i do agree that the seme saying "but i wont tell him that" does seem to imply what you said.
Maybe in the original language version they made it more clear Dx
Its not explicitly but im pretty sure it was implied that the dad is the yakuza. Rememvmber that before dating the uke, she was sad drunk because the man she loved rejected her even though she had slept with him. (That would be when she got pregnant).
And then we learn it was the yakuza that she loved. And the yakuza wanted to take the child and her not wanting a dna test because none of the 2 were the dad.
But what i find odd is we didnt get a single clue as to when and in what circumstances she actually started dating the yakuza.... and at what point did the yakuza knew he was the dad? And how come he didnt even try to take his child....