SpaceSet is already a list, so appending it creates a list of sublists. In order to keep spaces as nested lists you would need to append to two separate lists. One for each zone, and one to append the zone lists to a final “output” list.
zones=UnwrapElement(IN[0])
output=[]
for i in zones:
spaceSet = []
spaces = i.Spaces
for j in spaces:
spaceSet.append(j)
output.append(spaceSet)
#Assign your output to the OUT variable.
OUT =output