What the fuck is the goddamn malfunction, numbnuts?!
(And I'm using numbnuts as both a literal description as well as this MC being a fucking idiot.)
"I am so sorry, but you look exactly like my little sister," isn't impossible to say; I just typed it, and it's even easier to say it.
Nobody is saying you have to add "... and I've been allowing you to call me 'onii-san' because I miss her," but you can still say that, if you want.
The most fucking stupid thing I've ever read in any manga is the MC saying: "I can't tell them/him/her that."
Because you absolutely CAN tell them this, every single time; you just don't WANT to tell them.
... And the only reason you "don't want to," is the author being a brainless fuck who's never spoken to another human being as an equal before.... and thinks it's normal to lie for their own convenience.