While I don't love that line and it is used way too often in BL, I feel like it can still be meaningful and something to identify with for some people. Labels like "straight", "gay" or "bi" are so strict. Maybe people who think like this are "bi with a strong preference towards opposite gender", so they have basically considered themselves straight for most of their lives and a label like "gay" doesn't really match their identity, nor even just "bi". In this case Senpai doesn't like Shibamoto because he's a man (that is, because he's a gay guy who only could like other men), he likes Shibamoto because he's a cute person (and not just shallow, physical cute as an object, but his wholebeing, including his personality).
Not everything needs a label. Sometimes we like people because of who they are, not because they match our sexual preferences. We define our own experiences. If a guy once loved a woman, truly and honestly loved her, but has since then realized that he is sexually attracted to men and he is not interested in women anymore and that he is, in fact, gay, it's no one else's business to tell him that that one woman makes him bi. Liking one man doesn't automatically make you gay.
All that said, luckily openly gay and bi characters are fairly common in yaoi manga already, and they are becoming even more so. I hope the trend continues. Some characters expressing this sort of confusion (and it can be confusion, people don't always speak in absolute truths) is actually somewhat realistic.
Sorry for the rant! I was just already thinking about this because of an online conversation I read today about someone feeling uncomfortable because people around them were convinced that this person was gay, while the person had started to wonder if they're actually asexual. Most people told them that the label is unnecessary and that they should define their sexuality however they felt was most comfortable and accurate in their own experience.
I really wish BL authors would quit feeling the need to add a "no homo" line to their stories so much of the time. throws me out of the story.
"It's okay to be gay! " or bi, or whatever!