1. We are talking about a specific museum because of le (and not un). Du Bronze is used to mean the museum is related to that metal, here likely presenting objects made from this metal. An hypothetical Musée de bronze would be a museum made of bronze but about anything.

2. Yes, de is used here to express a belonging relationship.

3. Not here. La maison de poupée meaning is more “(An) house made for (some) doll(s)” so it doesn’t necessarily belong to any doll. Should it be the case, that would have been la maison de la poupée.

The same difference exists with une école de garçons (a boy’s school, i.e. a school made to instruct boys) vs l’école du garçon (the school the boy is attending, i.e. the one that “belongs” to him.)

Usually, the shorter a word, the longer its dictionary entry is and de is no exception: have a look to its TLFi one…

Adding on the good answer from Jiliagre: "du" is the contracted form for "de le". Whenever you would say "de le", it needs to be contracted to "du". It does not alter the meaning of "de" in any way. You will see the same contraction with "de les" which becomes "des".

la maison du voisin (for la maison "de le" voisin)

la maison de la voisine (no contraction for that one)

la maison des voisins (for la maison "de les" voisins)