Matt Thorn offers a couple of explanations. One is historical; Hagio was directly inspired by the tragic romanticism of Jean Delannoy's 1964 filmLes amities particuliéres, about two boys who fall in love at a boarding school. But Thorn also suggests that there were formal and thematic reasons for the choice. Hagio actually initially tried to set the story in a girls' boarding school—but found that she ended up wanting to make the action, as Thorn says, too "realistic and plausible." The result was, in Hagio's words, "sort of giggly." Thorn concludes that "It was important that the characters be Other in order for Hagio to explore the themes, some quite abstract, that she wanted to explore."
I don't disagree with Thorn's analysis of Hagio's motivations, but I think it's worth thinking a bit more about why and how it's important for the characters in Heart of Thomas to be Other, and why that would be something women respond to. Specifically, I'd argue that a big part of the appeal of setting the comic at a boys' school is that it allows male, European characters to be objectified, just as Asian women often are in Western fiction. In a lot of ways, The Heart of Thomas is an Orientalist harem fantasy in reverse. Instead of a Westerner thinking about veiled maidens on cushions in some distant palace, the Japanese Hagio fantasizes about beautiful boys in an exotic Europe.
The genre of boys' love, in other words, allows Hagio and her readers to place themselves in a position of power and aggrandizement that is rare for women—as the distanced, masterful position, letting his (or her) eyes roam across variegated objects of desire. It is, then, perhaps, no accident that the villain of The Heart of Thomas—a boy named Siegfried—is distinguished primarily by his interest in the Renaissance and by his odd, octagonal glasses. Siegfried's fetishization of old Europe parallels Hagio's fetishization of contemporary Europe; his dangerous gaze parallels Hagio's dangerous gaze. And Siegfried's abuse of Juli, the protagonist, is congruent with Hagio's own stylized sexualization of her characters. His desire is her desire—and also, perhaps, the desire of her readers. Thus, the prurient fan-service which is usually doled out only to men is here explicitly taken up by women, who get to watch more exotic male bodies than you can shake a spectacle at.
But while Hagio may be Siegfried, she isn't only Siegfried. Rather, the primary emotional point of identification in the book is Juli, or, more precisely, Juli's trauma. That trauma is, again, sexual trauma—or rape. In this sense, the book does not emphasize, or insist on the distance between characters and author or audience. Instead, Juli's rape emphasizes the universality what is often presented as a particularly female experience. Similarly, Juli's shame, his self-loathing, and his tortured effort to allow himself to love and be loved, are all character traits or struggles which are often stereotyped as feminine. The fact that Juli is male seems, then, not an aspect of otherness, but rather a way to underline his similarity to Hagio and her audience. If readers can with Siegfried experience distance as mastery, with Juli they experience an empathic collapse of distance so powerful it erases gender altogether.