That is correct. The problem is though that you need a Hapsburger to be relatively tollerant towards protestantism, while his Austrian and Spanish relatives will be pushing towards less tollerance. Will he be able to control himself? Hapsburg history speaks against it, but he is far away from the pope and his relatives so he might be.
Another problem is that a large part of the Netherlands isn't terribly happy to be part of the Netherlands; they would rather do whatever they want. This is true for the areas that Charles V conquered (Gelre, Friesland, Groningen, Overijsel) but the same is true for a place like Holland. They will still resent being ruled by one ruler, wether he is Spanish or he rules from Brabant. They will rebel the moment they don't think they are getting what they want and they will get support from neighbouring regions, like France, England, or German states like Cleves/Julich/etc.
A Dutch ruler will have a hard time and needs to be a great diplomat and this is a hard age for any ruler with the rise of the cities and merchants, the decline of nobility and appearance of protestantism. Sure a civil war isn't unavoidable, but you need a lot of skill as a ruler.
It also depends on
Yes, I can certainly see the Hapsburg Netherlands falling into the sort of multi-decade religious/civil war that afflicted France around the same time. The longer it goes on, and the more the protestant side gains (with Holland, Zeeland, and Antwerp, they will probably have the advantage) the more likely it is that either 1) The ruling Hapsburg monarch (or his heir) agrees to convert to Protestantism, or 2) the Protestants find some relative of the Hapsburg monarch to be a pretender. Whichever "side" wins, I think we can all agree that both will still have significant political power, and will have to find some sort of modus vivendi that they can both tolerate for the Hapsburg Netherlands to survive.
To the whole Holland deal yes I agree they didn't like external influence, and in general the Netherlands was just greater Holland. But there's a few aspect which should be remembered Karl V left Holland alone so much that the conquest of Gelre, Groningen, Overijsel (and earlier Utrecht) was complete financed and lead by Holland. If the Emperor are smart he leave them alone and only call to them when he need to extent his influence in the area. Especially because he can get more than enough money out of Brabant, Zeeland (was very rich until the collapse of the Rhine trade in the 80 and 30 year war) and Flandern where his control was a lot greater (to say nothing of his other possesions). So Holland will likely be force the Emperor use to "free" Münsterland from Protestant oppression (after which it goes the way of Utrecht, which was a former ecclessial estate). Ironic the fact that Holland get interest and power in Münsterland will make it easier for the Emperor to control them, because they don't want to lose the money they have put into conquer it.
Thought Munster was a Bishopric, unless your talking about the Anabaptist rebellion. But that was the 1530s, and Charles V's second son will just be a baby then, so I think this would unfold more or less like OTL. Though if the Netherlands' monarch later converts to Protestantism, he might try to free it from "Catholic oppression". The idea I had in mind was for the Hapsburg Netherlands to gradually expand into its south and east during the 16th-18th centuries, eventually taking or inheriting (among other places) Munster, Oldberg, Julich, Cleves, Mark, Berg*, and Trier. This would give alt-Netherlands several times the territory and population of OTL, allowing it to be a world power in a way our Netherlands never really could.
*If I'm not mistaken, these four territories make up the Ruhr, the ownership of which would be hugely beneficial to alt-Netherlands after the Industrial Revolution
Yes I agree it take skills, but only mediocre ones, only Philip II fanatism and lack of understanding of the Netherlands let him alienate enough to a full scale revolt. So long as the Alt. Emperor know his limitations, he can make it work.
Don't know, I suspect there would eventually be a blow-up of some kind. The Hapsburg Netherlands will have to adopt some degree of religious toleration no matter what faith the government is.