Currently when having different nodetypes displayed in the tree, the sorting just compares the name of the nodes, so when dealing with e.g. folders it doesn't look like it used to in 4.5.
making it configurable by allowing to define a custom Comparator seems to be pretty straight forward as we have the definition available:
info.magnolia.ui.workbench.tree.HierarchicalJcrContainer.ItemNameComparator