Good idea about the startup-sequence, with AfA One I used to create a standard installer that would install or overwrite all the files.
The problem is that when there are new settings or moving folders, I do it to have a logical order, in that case it's better to reinstall everything from scratch.
I wanted to create bootable DVD/USB like I did with AROS One x86, but on Real Amigas this thing is not easy to do, moreover installAROS seems to have problems, have you ever tried to install AROS with the new Nightly Builds on a blank HD either with WinUAE or with a Real Amiga ?