Bart had a romance with Jason (Victoria Atkin) when the troubled student arrived in the village as Jasmine last year. However, their union came to an end when Jason revealed his desire to live life as a boy.
Since the break-up, Bart has fallen for feisty Sinead O'Connor (Stephanie Davis) - but his feelings for Jason are revisited in next week's episodes.
Speaking to Digital Spy about viewers who want Bart and Jason to get back together, Clarke commented: "I think it's a very good thing. It's a very gritty storyline and I don't think you'd ever normally see two characters like that come together and try to make it work.
"So I can understand why there's a lot of fans supporting the two of them. I think what the storyline is showing is that it doesn't matter what you are, it's who you are inside that people are going to care about."
Discussing Jason's transgender plot, the 19-year-old continued: "It's groundbreaking for soap, because nobody's ever tried a transgender story like this before - especially focusing on a transgender character who's at a very young age.
"It's a pleasure to be involved in it. It was really nice that I could be involved in this storyline straight away - as soon as I started at Hollyoaks."
Clarke joined the cast of Hollyoaks last summer.
> Read our full interview with Hollyoaks star Jonny Clarke
> Read bonus bits from Jonny Clarke in Soap Scoop
Watch a teaser video for this week's Hollyoaks episodes below: