If a 110 spindle yields a 45mm chainline, then all other things being equal, a 113 spindle would give you 46.5 - not 48. Maybe you realized that, but it wasn't clear from your post. I can't imagine that this is your issue, as long as you're within the range provided by the limit screws. The longer chainstays on Rivendell bikes are more forgiving in terms of chainline variations. It doesn't need to be perfectly in spec because the chain isn't being forced to flex as much between disparate chainring/ cog combinations.
On the other hand and if I'm visualizing correctly - you might be better off using any derailleur in the bottom/inner part of it's allowable swing range, because the arc will be less "vertical" between adjacent chainrings. But I guess it depends on the geometry of the specific derailleur - whether it's top swing, bottom swing, how long the arms are, etc. If you're having trouble because the angle between the seat tube and chainstays is non-typical, and the chainstay is keeping you from mounting it as low as you like, then you're looking for something that moves side-to-side with the least amount of up-and-down. Some pics could help us armchair a diagnosis a lot easier.
Other random thoughts:
Shimano made some "side-swing" derailleurs that had almost no vertical movement, that I've used for this precise chainstay clearance problem, but it was much more of an extreme combination of factors than you're dealing with. Also, the cable routing is wonky.
A couple of years ago, Bill did a detailed post about shortening the shift cage so it would have more chainstay clearance. Maybe he'll chime in or you can find that thread.
Lastly, Before spending a lot of time and money, you might want to measure the actual chainline yourself, to know what you're working with: measure from the center of the middle chainring to the face of the seat tube, and add half the seat tube diameter.