Kornshell 93 has a long list of commands built into the shell for performance reasons. So if you execute chmod in ksh93, you don't need the external chmod program. Sometimes you need to call chmod with a full pathname, but that is not much of an obstacle.
Code:
$ type chmod
chmod is a tracked alias for /usr/bin/chmod
$ type /usr/ast/bin/chmod
/usr/ast/bin/chmod is a shell builtin
(from Opensolaris' ksh)
I don't think, chroot will help you much in this case. The only solution I can think of, is to delete ksh93 or compile your own version without builtins - which will result in slower execution of shellscripts.
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