Maybe I'm being blind, so please forgive me if I am. But there doesn't seem to be a way to convert from the duplicated oil (after boiling then sent through the space matter refinery) to the original oil needed for recipes.

Looking at the duplication recipe, the refinery takes the oil heated to 165 C and creates oil at 60 C, but according to Factory Planner the "Crude oil (60 C)" is a distinct different item from regular crude oil, so it can't be used in recipes.

Does the space matter refinery actually produce the regular crude oil and this is just recipe weirdness?

This is an issue with Factory Planner sometimes not playing well with temperatures.

If a recipe does not call for a specific temperature or range of temperatures for a fluid, any temperature will work. Like the Crude oil Boiler consumes Crude oil (no temperature given), and generates Crude oil (Temperature: 165 °C). This can then be consumed by the Space Matter Refinery because it matches the ingredient description Crude oil (>= 120 °C). You could actually use the hot oil in the regular refineries if you wanted to since that doesn't require a temperature, either.