I think the seme's just an airhead. He ran into an adorable kouhai, maybe it was love at first sight, who would come to him whenever he asked. Admittedly he took the advantage of uke. (If we use cliches seme bullied he's crush) I don't think he meant to make uke lonely, he just wanted to spend more time with him. I think that it didn't even cross his mind that the uke could be lonely.
And since uke was so timid he couldn't talk back and that made the experience so much worse.
And about eating in the toilet, maybe seme knew that uke used to eat in the toilet and thought it was because he liked the peace and quiet or something. Maybe he didn't want to consider the option of the uke avoiding the seme, and didn't think it was because uke was lonely.
But all of these are just my theories to make the seme seem more lovable, awkward and now more suitable partner for the uke. Romanticizing!
See I don't know about this one.You did make high school a living hell for him and now you've changed? Nope even that toilet scene to, ughhh