Not really familiar with deluge, but for your
2)
-d, --home HOME_DIR
The new user will be created using HOME_DIR as the value for the user's login directory. The default is to append the LOGIN name to BASE_DIR and use that as the login directory name. The directory HOME_DIR does not have to exist but will not be created if it is missing.
-r, --system
Create a system account.
System users will be created with no aging information in /etc/shadow, and their numeric identifiers are choosen in the SYS_UID_MIN-SYS_UID_MAX range, defined in /etc/login.defs, instead of UID_MIN-UID_MAX (and their GID counterparts for the creation of groups).
Note that useradd will not create a home directory for such an user, regardless of the default setting in /etc/login.defs (CREATE_HOME). You have to specify the -m options if you want a home directory for a system account to be created.
I'm guessing You need to add a new user to run the program/script, because running is as root could potentially be dangerous and can jeopardize your entire server in case your program/script was vulnerable .