Another important point is that this also affects the order in which plug-ins are physically processed. That could be useful in some cases, in case one instance somehow depends on another.
After the feature of visualisting collection, this has stopped working. It seems that the GUI keeps its sorting order from when the instances gets added to the context, and ignoring any context reordering post-collection.
Have a look at adding a test for this in pyblish-qml. There are a few examples there to light the way. If a solution doesn’t pop out to you, I’ll try and take a look at this once the test captures the problem.