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Doesn't Jenkins fail to boot if it cannot write to its home directory?
A sane solution would be printing a warning if Jenkins is configured for a different user than owns the directory, or only chown-R'ing if the owner of JENKINS_HOME is different than expected – but not unconditionally. If only some files below JENKINS_HOME are owned by a different user, it's either intentional, or you broke it in some drunken craze, and I don't think the installer needs to fix it in either case.