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I stand by what I said—stories in and of themselves aren't gendered—but the way we market and talk about books often is. And even more so, the marketing is often (not always, but often) tilted one way or the other based off not the story, but the perceived gender of the author.
For example, let's take a look at some YA contemporary covers with romances, authored by dudes and ladies.
It's interesting looking at the mini-breakdown, because while there are totally exceptions, even though these covers have the same general audience (teens who like YA Contemporary with a splash (or more than a splash) of romance), there's a pretty clear difference between the covers for books authored by guys and those authored by ladies.
To start with, the books authored by guys rarely have a girl on the cover (and when they do, there are also boys on the cover). Even The Fault in Our Stars which is narrated by a girl goes for a more gender neutral (or even boyish) illustrated presentation without any figures on the cover. The illustrated covers for books written by ladies, however, do tend to have girls on the cover, or some kind of feminine indicator, like lipstick. Covers for books written by guys tend to be more illustration-heavy with less gender markers present; covers for books written by ladies often have photographic covers featuring a girl, often with who we assume will be her beau.
That's without looking at font or color scheme, and yes, of course there are exceptions (Jay Asher's Thirteen Reasons Why, for example, has a photographic cover featuring the girl protagonist), but it's kind of hard to ignore some of the not-so-subtle gendering of book covers based solely on the author's perceived gender.
This is one of the many reasons why female-identified authors writing speculative fiction sometimes use gender neutral pseudonyms (most famously J.K. Rowling)—even when the books feature a male protagonist, there's an assumption of sorts that (some) guys won't pick up books written by women, and I can't help but suspect the gendering of covers has a lot to do with it.
Of course, especially in more recent speculative fiction, there are a lot of covers that avoid gender markers entirely regardless of the gender of the author, which makes sense in order to appeal to a wider audience.
But in a world where AFAB (assigned female at birth) kids are taught to identify with characters regardless of gender and AMAB (assigned male at birth) kids are shamed for being too girly and largely fed a host of media for boys, it's no wonder girls won't blink at picking up a book no matter how "boyish" the cover seems, whereas some guys may hesitate to do the opposite.
Ultimately, in terms of writing, my advice remains the same: if you want to write a story that isn't gendered one way or the other (and it is totally valid, by the way, to want to write for an audience of one specific gender) then write what you want, however you want, and the right readers will enjoy it regardless of their gender. But it's also good to be aware, I think, of the ways a book is packaged can affect who picks the book up and takes a look inside to begin with.
From book packaging to the story inside, @Ava_Jae talks about gendering and books. (Click to tweet)