Yeah this is complicated. The processed fuel has its own category, and the machines accept both the chemical and he processed fuel category. The fuel doesn't show up in settings because it is not a chemical fuel, it's alone in its own category, and categories with only one member aren't shown as there is no choice to make.
There are probably a few solutions to this, but none I thought of thus far are very practical. The brute force one is to also offer every viable combination of fuel categories in preferences, but that's obviously a combinatoric explosion, and not worth it to solve this single case imo. Another solution is to hardcode the processed fuel to be part of chemical fuel, but that probably causes tons of exceptions to be required elsewhere, and I don't like hardcoding things from specific mods. Soo yeah not really sure what to do about this. If anyone has a good idea, please let me know.