EU IV has a specific time-frame, which I am bearing in mind. These groups won't all have a static penalty up until the Industrial age. Typically, this is going to be the case for groups that tended not to fluctuate scientifically until very late, such as for the Steppes and the Eastern Europeans.
American civilizations (Tribal and High) will both receive the most significant penalties, which will last until the Industrial Era. However, Tribal Americans will not receive these penalties during the Ancient Era, and High Americans will not during the Ancient and Classical Era.
Another case is Asiatic civs. Again, technological penalties will be limited to a confined time period - specifically, the Renaissance and the Industrial Era. Asiatic civs, I feel, should be the only group that are slower to catch up industrially that others (but the penalty will be fairly modest).
Ancient civilizations would not get a science penalty in the Ancient era, akin to the Native Americans, but, as I said above, would likely speed through them (and Graeco-Roman would speed through Classical techs), before stagnating in the Medieval and Renaissance, before being able to catch up in the Industrial Era (where it levels out for everyone but Asiatic civilizations).
Arabic civilizations are definitely an interesting case. This is why I especially like the faith into science idea, because it would be a way to simulate their scientific advancement during the weakest points in European scientific history, without giving them an explicit bonus to research during certain periods.
Europeans could, possibly, get a small penalty to simulate the Dark Ages at the beginning of the Medieval Era. However, here is where the fine line between realism and sticking to the game's "What if?" spirit starts to snap.
In any case, this is all tentative thinking. Feel free to keep offering ideas on the way science penalties should be managed (but I do intend to have them, regardless).