I agree with commenters that you're probably reading too much into this. Not every line of dialogue is pregnant with some deeply-layered meaning. Sometimes a sociopathic murder and a line of superficial wordplay is... just a cigar.
But, if you are desperate to find something here, I suppose role-reversal works in a pinch.
After receiving an excellent answer — which still hesitates about the last two lines —, I have tried to dig up more versions of this movie and see if indeed there is no clear version. I have found one, and now I have little doubts that the last two lines are:
Oh, isn't that lovely father, isn't it gay?
Why not? Weren't we born that way?
I have cropped that ...
Just from listening to it - a cleaner copy than the youtube but still pretty old & crusty - I can get most of it, but I'm uncertain on the very last line.
It's my sonata, isn't it?
I'd forgotten all about it.
It's most annoying of you never to finish it.
I tried to myself all sorts of ways.
Oh no darling you can't do it like that.
No, you ...
The main thing Tony remembers about Howard as a father is his absence.
Howard was much too busy with his company, and Tony wasn't really fathered much as a result. By the time of Endgame, Tony has seen the video Howard left for him, so he knows that Howard did in some way notice Tony, but Howard is still a very incomplete image from Tony's past. His business ...