The problem with treating specific manufactories differently is that you end up with very skewed results. Generally, people in multiplayer tend to build refinieries beyond everything else because of the increase in trade efficiency. I'd believe most single players use a similiar approach, although it of course is not the preferable strategy for inland countries with sucky trading (Prussia, Austria, Russia). Anyhow, since in such a game the big majority of the factories in the world depending on the refineries would be created, I believe there would an oversupply in those goods. This would result in these factories barely able to make a profit, and it would cause a chronic undersupply of all goods related to factories that were not converted due to that no such refinieres was built in EU2.