Storage House counts as remnant (Eruvin 60a)

Abaye says that in Pumpedisa they counted the storage hours of Bar Pupedisa as the remnant to allow them to make an eruv around the rest of the city. Rashi says that they were ablt to do this because we pasken like R' Shimon that you don't need 50 residents to consider it the remnant. How does it help that we pasken like R' Shimon - he still requires three chatzeiros?!?

Tosafos says that there were three chatzeiros together with this storage house - the point here is just that the storage house can count as one of them even though there are no residents. The Sfas Emes says that it doesn't sound like Rashi agrees with this because he doesn't mention that at all. He explains that it could be that Rashi didn't want to give that explanation because then that would be no proof. If Tosafos was right then the only thing we see is that the storage house could count as one of the houses needed but it doesn't answer Abaye's question if the entire remnant could be something that couldn't have been included. The Sfas Emes therefore explains that it must be according to Rashi the storage "house" included three chatzeiros of two houses each. My only problem with this explanation is why does Rashi say that we pasken like R' Shimon who says that you don't need 50 residents? Why doesn't he say it in the positive - we pasken like R' Shimon who requires only three chatzeiros?

The Rif though understands the gemara differently. He paskens like R' Yitzchok at the end of the gemara who says that you only require a single house (not like R' Shimon or the T"K of our mishna) and Pumpedisa likewise paskened like R' Yitzchok so there was no need for chatzeiros. Tosafos paskens like R' Shimon so he couldn't explain our gemara like that. The Rosh is bothered by this Rif - how could he pasken like an amora when there are tannaim who argue on him? We pasken like the Rif though.

I was thinking to answer the Rif and my question on Rashi that R' Yitzchok doesn't mean to argue on the tannaim but he just means to explain R' Shimon. He's saying that's what R' Shimon really held. Our mishna quotes him as requiring three chatzeiros but R' Yitzchok argues and says he only requires a single house. I'll admit that I'm not crazy about this explanation for a number of reasons.