I guess it just really comes down to upbringing, especially with people around you that can shape your thoughts on certain perspectives. And of course on how much you can handle and process it. I had internalized homophobia for a year when I discovered I liked a girl, but I was second guessing myself because Its out of the norm and just seems weird to like the same gender, but I've come to accept my own sexuality. Seeing as how Eugene grew up being mocked, and bullied in a way, he's the type of character that is more prone to try and fit in as much as possible of course thats just my own take and understanding and does not apply to everyone.
you explained it very well
as a gay guy around his age, looking at eugene's character is so shocking cuz i cant imagine having internalized homophobia... i have never doubted who i liked and have never been scared