When I create machine axis change it is absorbed by prev. tool change and it becomes less readable unless tree is fully expanded. Also I try to put a pp instruction before machine axis change by putting some disply or pprint statements, comments etc. Idea is to keep the tree organized and documented. I have used other systems in past such as mastercam, ug, surfcam and I was able to keep my programs fully documented. UG allows you to view the tree in either tool order or mo order
I think whenever any cnc-programmer starts building toolpaths first thing he thinks what tools will be used for that particular op and then start using them in mo. Once the program is done all you want to see machining operations in sequential order. And then in final review you can rearrange some mo (especially when some 56 tools and 120 mo used) just by dragging them without creating the tool-change.