Would you consider doing an AU of this story with the same set up except tommy is endowed normally and thus its a more traditional nerd + jock romance where James can be an alpha top and protect tommy from bullies. Its just that the way you described both of them is so hot and not that I didn't think the twist but it seems like a shame not to also do a more traditional set up with them also ( maybe with some muscle worship thrown in given the size difference and how unusually humble James is given his size like maybe have tommy encourage James to show off and have James flex to flirt with tommy and make him feel special ) if you think its dumb that's fine I'm just speaking as a sucker for nerd\jock romances ( unsurprisingly I'm a weak nerd myself lol )
Most nerd/jock stories fall into such categories, but my story was meant to be a different, rarely explored take, where the trope of an alpha being dethroned by someone even more of an alpha is tweaked. While most stories of this nature have the new alpha outclassing the old alpha in terms of strength and endowment, here the new alpha only outclasses the old alpha only in terms of endowment. As such, Tommy has to have enough endowment to make up for his lack of strength, though Tommy DOES demonstrate a deceptive level or strength (like in the planned reboot, the continuation would have elaborated that this is when he is aroused). He's basically an unconventional alpha male. Taking away his endowment would make him equal or even lesser than James, which completely throws the story in another direction.
I did, however, write a story about an 18-year-old who is shown to be a major late bloomer that has a few of the ideas you touched upon. It's called "Piglet Lawson" and has a proverbial "runt of the litter" late bloomer having a sudden "blooming" after fooling around with a hunky alpha archetype named Mercutio. Like your proposed version of James, he protects the main character from bullies and demonstrates a greater level of benevolence towards weaker people.
Also, if you've read "My First Day at Donkey Dong High", you might see how I was inspired by it. I just took on the concepts explored in a different direction. I hope I'm not spoiling anything.
Then there's the fact that the whole thing is nerd wish fulfillment. How many skinny geeks wish they had big fucking godcocks large enough to make the buff bullies that torment them drop to their knees and relinquish their illusions of superiority, or in the case of heterosexual stories of this nature lose their girlfriends to some scrawny geek with a monster in his pants?
And finally, you hardly ever see a big muscle stud bottom for a skinny nerd unless the former has a small dick (there's a video that fits this bill out there, but I can't remember what it's called but I found it on the "Big/Small Comparison Thread"). By giving the jock a huge cock we make it seem like we know where this is going, only for the twist to be introduced.
But that's just me. Also, iirc 50 Shades of Grey started as Twilight fanfiction, so if really wanna see what you've described why not give writing a try? It's not easy, though as someone who basically just drummed everything out on the fly I probably just make it seem easy (it's not). I've been dying to get back to writing stuff like this, whether for LPSG or self-publish (can I publish such hardcore gay smut on Amazon? I know there's "gay erotica" on there but my stuff and the stuff on there are two different worlds it seems).