yes I do believe itunes can no longer backup your actual apps using 'transfer purchases' due to 'app thinning' or something like that. Believe ifunbox or itools can still do it but not sure if it requires a jailbreak
the only one true system image on mobile devices is a nandroid backup! (custom recovery required)
iOS only backs up user data, no system (no downgrading ios) - mostly semantics I know, but you cant have a system image without the system

It restores the latest OS from apple, then restores your userfiles in the local or icloud backup
if we were able to create system images on iOS (and be allowed to restore them) that would offer complete freedom, a dream come true!