He pulls an emiyaand charms rider and caster and they take up the guest house as a place to live which is mostly used for sex
Ah, OK.
Well, can't they "punish" Caster as part of that? It's not like the punishment won't be enjoyable....
Anyway, I have an idea for a possible setting. It's a universe in which slavery is widespread. In particular, traditionally women have been seen and treated as slaves (although there are also male slaves around). Much of the world has given women the ability to be free, and some of the more enlightened parts have abolished slavery entirely, but in Japan all women are still slaves and cannot be given freedom (except for foreign visitors, who are given a special exemption).
Sakura and Rin are Shirou's slaves, having been taken as "spoils of war" by Kiritsugu, possibly along with their mother, after the fourth Grail War. However, since Shirou isn't a dick, he treats them kindly, and also refrained from having sex with them until they were old enough. As a result, as of the Grail War he's had Rin as a trained sex slave for about a year, and is in the process of training Sakura. Despite being slaves, the two girls are quite assertive (Rin in particular is prone to "topping from the bottom") and generally much like in canon (Sakura is actually more assertive than in canon because she's not been abused by Zouken for eleven years), and Shirou is OK with this because, as I said, he's not a dick, and he also cares deeply about the two girls, who have grown up alongside him from the age of 6 or so (they've always been his slaves, but he's never been mean or abusive towards them). He is, however, still clearly the dominant one in their relationship, and there is quite a lot of BDSM involved (although not always). However, they are also somewhat prone to making rash decisions and mistakes, and thus he does expect them to obey orders when it
really matters, and not to do stupid things, and if they do so they will be punished for it.
I'm not sure how Shirou got hold of the girls, exactly, but Rin would still have the Tohsaka magic crest, and both sisters would be training in magic. The idea, at least nominally, would be for their first-born son to obtain the Tohsaka crest to continue the family line. Shirou is OK with his role in things (because Sakura and Rin are happy, and Sakura is if anything jealous of her big sister for getting to fuck Shirou earlier), but is a bit unhappy about the system more generally, because not everyone is going to be so nice to their slaves.
Just when he was about to start training Sakura, the three of them receive their command spells for the Grail War. Shirou knows he has to win the war, because failure to do so will mean Sakura and Rin will be taken as spoils by the victor, and likely treated much less kindly. So, he is a little harsher with Sakura's training than he otherwise would be, in order that she will be safe during the War, and not allow herself to be captured. The house would be mostly normal, but would have a built-in dungeon area for him to use to punish the girls if necessary, or even just for playing sex games (which the girls are quite OK with).
In particular, I'd have Shinji or Zouken summon Rider, with Shinji intending to take the Tohsaka sisters as his own slaves. Sakura would get drawn into a trap of some kind (by going out without her servant) after Shirou told her not to, and would be held hostage by Shinji with Shirou being told to surrender his command spells or she dies. Fortunately, she's able to be rescued, and Shirou manages to obtain Rider somehow. However, Shirou is very annoyed with her (because of the danger she put them all in) and she's annoyed at
herself. So, he enlists Rider's help in punishing her harshly for her screw-up.
I've not fully worked out the world yet, but I suspect the Grail War would have more servants. I'm also not sure what would happen with Ilya, since bringing her to Japan in this timeline wouldn't be particularly wise, and she also makes Shirou too powerful. For other masters, I'm thinking that Luvia would be one, with her goal being to capture the Tohsaka sisters (her family wants to enslave and torture them, and they have a dungeon ready and waiting), and Bazett would also be one. Both of them would be from countries where women aren't necessarily slaves, and indeed would probably own slaves theirselves. I'd imagine Gil/Kotomine would also be around, with the general intention of causing misery etc. I also considered the option of making the Grail non-corrupted, although that does change a hell of a lot.
I'd also have the Tohno family involved. In this timeline, Shiki would be the family head, and Akiha would legally be his slave. However, Makihisa would have set it up so that she actually has a hell of a lot of influence over him, and is essentially in control. Kohaku and Hisui would just be Shiki's slaves, although he wouldn't be nasty to them. They're also fighting for the Grail, but they're quite happy to take on more slaves if necessary.