At first use you must set a new password for flexget using the command line:

sudo su -s /bin/bash sc-flexget -c '/var/packages/flexget/target/env/bin/flexget -c /var/packages/flexget/var/config.yml web passwd <MyPasswd>'

Using your browser at http://<mySynoNASIP>:8290 and login as user flexget with your newly associated password.

From there follow https://flexget.com/Configuration to complete your configuration.

It looks that all command line use of flexget has to be done as user sc-flexget and need explicit parameter for the configuration file.

I.e. to call flexget trakt auth <account> you must use:

sudo su -s /bin/bash sc-flexget -c '/var/packages/flexget/target/env/bin/flexget -c /var/packages/flexget/var/config.yml trakt auth <account>'