My research seems to suggest this should be possible given this helpful post
@master007:

I wanted to check out the config file too… Didn't find ntopng.conf.
The package uses a different method to configure that service in pfSense.

Here is what I found:
there is 2 files related to ntopng in
/usr/local/pkg/ntopng.inc
/usr/local/pkg/ntopng.xml

This file :/usr/local/pkg/ntopng.inc seems to have all the logic for configurations included.
and seems to start ntopng on the fly with config parameters based on the the xml config file / web page

It starts something like this
(after looking at ps -A)
/usr/local/bin/ntopng -d /var/db/ntopng -G /var/run/ntopng.pid -s -e -w 0 -W 3000 -i em1 --dns-mode 0 --local-networks 192.168.0.0/16,172.16.0.0/12,10.0.0.0/8

Perhaps that info helps you further...

in the .xml file it seems pretty straight forward to add a box that would show up in the ntopng settings page and take the custom line. That field then just needs to read and added to the startup line in /usr/local/etc/rc.d/ntopng.sh when it is auto generated by the service handler.

Im a fair noob so that's about as far as I could get, any help would be appreciated, and it seems this would help a number of other people too. What is actually building the /usr/local/etc/rc.d/ntopng.sh file. I assume it is run everytime save is pushed?

Cheers