It's not even that I want to see it, and I can easily imagine why this didn't happen, since I don't think I've ever seen him featured in any doujin, but I notice there's one Servant in the harem that Rin was not intimate with...
pg7 - "No matter what world I go to, my boobs are always so small..."
As a weirdo that likes the idea of a large-breasted Rin and therefore seeks out such things (it's something annoyingly uncommon TBH 4-years later UPDATE Interestingly it's getting more common in fan-works now?), I think I have enough experience to say that the depiction of Rin in this doujin is actually somewhat bustier than most
Nevertheless, maybe the trick is that it was the Matou mana and Zouken's worms that "blessed" Sakura with her sizable breasts, therefore the issue is that Rin is simply looking in all of the wrong places - she needs to go to an alternate timeline where she's "Matou Rin" and Sakura remains in the Tohsaka family (which, regardless of breast size, is something even more uncommon than just plain old "busty Rin" surprisingly enough despite the whole idea of multiple alternate timelines being canonical in F/sn)
EDIT:: To add weight to this theory, I came across a great comment by "Andrew Greaves" on a Matou Rin / Tohsaka Sakura fanfic titled "Different Fates v3":
EDIT 2: Digging farther into the comments on the very same "Different Fates v3" fanfic reveals more theory-crafting that Sakura's larger breast size could alternatively (or perhaps additionally) be due to the Edelfelt genes in her due to the Tohsaka-Edelfelt genetic connection.
This could farther point towards the idea that Rin is simply looking in the wrong places because I would imagine that Rin would find the idea of having even more Edelfelt genes to a complete non-starter, and the same undesirable-ness applies to the idea of having to deal with Matou's worms as well (or worse yet for Rin, a single timeline of having more Edelfelt genes 𝑎𝑛𝑑 having to deal with Matou's worms!)
Rin's small boob size is probably due to some malnourishment. Specifically having to work with Kirei's eating habits and due to skipping breakfasts.
Contrast that with Sakura who started going over to Shirou's house when she was around 14 1/2. She was getting 3 full meals a day pretty much for a good while, right at the beginning of puberty for her. Thus she got more nutrition.
So Rin probably got fucked over due to her own eating habits and due to how Kirei ate.
It's also mentioned (at least in the VN, no idea about the anime) that Sakura has been concerned about her weight and general over-eating, so you may be on to something there.
And like I mentioned above, it could even be a combination of various factors - for all we know maybe it's the combination of being "well fed", getting the right Edelfelt genes, and the "Matou worms" that all came together to create such a difference in boob size in Sakura compared to Rin.