What i mean is a user could have replaced libraries or other system files such as MUI classes or modified s-s or be running some 3rd party software...
It is always possible... nobody knows what those installer scripts are doing. Problem is user can not really know is his install clean or not.
To quote your reply to tmhgm:
Does it not backup your mossys: directory and install a new one every time, even if you do an upgrade? I don't really see your point. MorphOS is coming as full releases, and not update packages, so obviously there will be a difference.
You can choose to update or install as new. If you just update you can keep your old settings, user-startup (while s-s is replaced), fonts, libs, classes, almost everything you have installed outside mossys: is kept intact. User can update from any previous version without installing any intermediate patches.
If update goes wrong you can always restore your previous mossys: what is also useful when testing iso images.
That's a design decision. It has its good points and weak points. One weak point is that you have to download an entire ISO, burn it, just for the "updates" to go from 2.6 to 2.7.
You dont have to burn it (although I recommend it). You can just mount it and install from there.
Again this is a design decision, and may have been influenced by the fact that the MorphOS team didn't work from the original source code, so they separated all their things in their own directory, rather than directly updating the components themselves (because they didn't have access to them. Effectively you have two sys: assignments which is not required for OS4 since it *is* the original.
Nothing prevents you using OS4SYS: or maybe even implementing different scheme. Neither did AROS components (i.e. locale.library) support mossys: either so it was retrofitted where needed.
Oh, btw, MorphOS 0.x versions didnt have mossys: assign but it directly replaced original components. (Due to this legacy MorphOS is still trying to load #?.library.elf first.)
