I had a really hard time to discover how to configure the system. The switch to plugins means that the settings are just all over the place and the help pages are still rather chaotic. I gave up because I could not discover how to setup different taxes for product categories or per product.
You may have looked "everywhere" but I haven't seen you on the very active forum. It is true that a switch to plugins means a little more work for the user, but the benefits are clearly huge. I would have like to see you on the forum where you can freely ask your questions and in 99% of the cases get your answer.
Settings all over the place, same as for Joomla, Plugins have settings in the plugin config and in the plugin parameters. Component has global config in one place. I'm not sure what you mean with "all over the place". As for the taxes setup, the forum is your friend.