Happy Valentine's, and you asked me a question, I will answer it, so please do not ignore.
"Unless you mean to say that the ship itself should be his beloved?" You are 3000% correct. As for what drove me to lash out at you before, just ask yeaka.
I'm still not entirely sure what you're aiming to accomplish, hon - but if it's to accuse me of plagiarism, you are seriously barking up the wrong tree. Likewise, if you're angry that I dared to write Khan with an Original Character rather than someone from canon, I truly don't give a fig.
I work in a field where I have to deal with strangers being dishonest with me nearly every day. So much so, that I know a lie within a few moments of our conversation starting. When I share with other folks the myriad ways that Liars have devised to rip off a retailer in the course of returning something, they (as I used to be) are shocked to learn the many ingenious means of deception. My reply is always, 'Well, you wouldn't think of something like that because you're a honest person'. And likewise, it never occurred to me to look up the word 'yeaka' as I figured it was a typo, rather than a basis for an accusation.
However, one of my dear tumblr friends thought to look it up and discovered it's an AO3 penname of someone who writes Khan fic, shipping him with various canon characters. For the record, I don't recall ever reading anything of theirs - nor have I visited their works now out of curiosity. I didn't think to look for myself as some means of defense because I am simply NOT A PLAGIARIST. Every fic I've published is based on my own imagination, including those that resulted from RP with partners who granted me permission to write them.
If on the other hand, you simply can't tolerate shipping Khan (or any canon character) with someone non-canon, I'd advise you to keep to your own lane and block tags for fics that may raise your ire. If you're curious, though, you might discover there is a wealth of fics featuring OCs, as well as stories featuring crossover characters from completely unrelated fandoms. Make a quick search of 'Khanlolly' alone, and you'll find many, many stories featuring romance between Khan and Molly Hooper from BBC Sherlock, basically because he wears Benedict's face. Khanlolly is an offspring of the Sherlolly fandom.
In short, fan fiction Authors are free to play with whatever characters they want in whatever manner they choose. As of today, there are no fic police to restrict what can and cannot be written. If you don't like, don't read. That will ensure peace of mind for everyone involved.