I don't think papal influence really works. The beeldenstorm happened in Flanders, so there were significant numbers of people who were Calvinists like the Dutch. There is a significant likelihood due to their position that they'll end up Protestant or Reformed, so papal influence is kind of useless. I made the priority trade and naval with a little colonization and a little military for good measure. I really don't like papal influence in idea sets, especially for countries with a history of religious diversity. I think the toleration fits a lot better, because there were a lot of foreign merchants of many different sects that resided in the major cities of Flanders. Sure, there were a lot of Catholics, but the reformation hit Flanders just as hard as everywhere else in Northern Europe. The Calvinist Dutch and Lutheran Hanseatic merchants were embraced by many of the trading elite, as were their beliefs. Without the Spanish there to enforce the Catholic orthodoxy, the situation might have been significantly different.
Additionally, I represented Flanders (and most specifically Antwerp) as a major cosmopolitan center of trade with the +1 merchant tradition. By the start of the game the cloth trade had significantly waned in importance, and wasn't really a factor after Calais fell to the French. The much larger trade value at the time during the game comes first with the rush on Portuguese-imported pepper and cinnamon in the early 1500s, and then moves on with the emergence of sugar as a commodity and Antwerp as the main sugar port in Europe (thanks to the Spanish colonies), which is absolutely huge in terms of importance.