The directory /home/chroot/bin is not of interest for ISPConfig, as the users where chrooted to their home directory which is not /home/chroot/.
Please post ls -la from the home directory of one of the users.
I am kind of confused about the use of the chrooted /etc/passwd and group files. ISPConfig doesn't update them when I create or edit new users, rather it updates the system proper /etc/passwd and group files. Is that correct behaviour?
Yes. Because other users that you edir are not of interest for this chroot enviroment.