Note: I'm dutch, so this is written from a dutch perspective.
For the last few decades, there is a transfer of wealth going from Flanders to Wallonia. Not surprisingly, a significant part of the Flemish population would like to reduce that transfer.
Independence of Flanders is an extreme way to stop the transfer of wealth. If there aren't enough reforms to reduce the wealth transfer, Flanders might go that route. Like the Brits did with Brexit.
The counter argument against Independence of Flanders usually is that Flanders can't survive on its own. The counter of that counter is the union with The Netherlands: suggesting that Flanders would be better off as part of The Netherlands than as part of Belgium. The whole idea of joining The Netherlands should be seen in that light.
Whether Flanders and The Netherlands would join afterwards, well, I doubt that would happen in practice. Flanders is economically strong enough to survive on its own. And why would one join distant bureaucrats directly after breaking away from some other distant bureaucrats?
Note that the southern parts of The Netherlands are culturally closer to Flanders than the average in the Netherlands: Those parts are Catholic in origin, like Belgium and unlike the rest of the Netherlands. However, history since 1830 has been different for both countries. Especially the memory of WWI (1914-1918) is very different: Belgium was part of the front line and heavily hit, while the Netherlands remained neutral and mostly unaffected.
As a result, to me - a dutch citizen - Flanders feels like a different country than The Netherlands. Closely related, like siblings, but a different country nevertheless.
Close cooperation on many fronts likely would happen. We do that already on the national level - see Benelux - and there is lots of cooperation at the local level.
I also expect some opposition in The Netherlands against a full union. The Dutch harbor of Rotterdam is a historical concurrent of the nearby Belgian harbor of Antwerp. Antwerp is also connected to the North Sea, but that connection is controlled by The Netherlands. The Netherlands has used that to disadvantage Antwerp, e.g. by dredging as little as possible and by stipulating it an "environmental protected area." Unification would make that impossible. Sometimes politics can be that petty.
To get back to your question:
But which of the alternatives would they prefer (in majority):
Any alternative that reduces the wealth transfer. A loose Federation within Belgium if possible, Independence if necessarily.
As a bonus, an answer to this question:
That is, purely hypothetically, would it be possible for the Netherlands to annex another region, if it was with the consent of the local people and that of the Belgian government?
That's not hypothetically at all! We recently did (link in Dutch) - nobody lived in the areas affected, though. The red part became Dutch, the yellow part Belgium. The dark parts are water, including the river "Maas."
Although the situation in the village Baarle-Nassau, where the border is very complicated and neighbors might live in different states, hasn't been resolved yet. I guess it doesn't cause enough problems in practice.