I'm not much of a network guru type TBH so not sure if I can be any direct help with networking issues but I know a fair bit about TKL so hopefully I can be some help! :)
Confconsole isn't interrupting the boot process. By default it auto runs when booting has finished. As TurnKey is more-or-less intended as a headless server, interactions are more often than not via web browser or SSH (depending on preference). So many (most?) users only see the confconsole screen when they first install and setup - so in that context it makes lots of sense. No reason why you can't remove it if you'd prefer though (as it sounds like you've done). Perhaps ideally it should be an option in confconsole itself?
IPtables is what TurnKey uses behind the scenes - Webmin just provides a UI for it (and calls it 'Firewall' instead). If you'd rather directly interact with IPtables via the commandline then that's an option too. Also FWIW by default it's not enabled (i.e. it is configured to work OOTB if you do enable it; but is disabled by default).
Network config can be handled with confconsole (just the basics) or Webmin (a lot more options) but beyond all that TurnKey is a customised headless Debian under the hood. So it can be configured via commandline just like any other Debian server.
Not too sure about networking...
Confconsole isn't interrupting the boot process. By default it auto runs when booting has finished. As TurnKey is more-or-less intended as a headless server, interactions are more often than not via web browser or SSH (depending on preference). So many (most?) users only see the confconsole screen when they first install and setup - so in that context it makes lots of sense. No reason why you can't remove it if you'd prefer though (as it sounds like you've done). Perhaps ideally it should be an option in confconsole itself?
IPtables is what TurnKey uses behind the scenes - Webmin just provides a UI for it (and calls it 'Firewall' instead). If you'd rather directly interact with IPtables via the commandline then that's an option too. Also FWIW by default it's not enabled (i.e. it is configured to work OOTB if you do enable it; but is disabled by default).
Network config can be handled with confconsole (just the basics) or Webmin (a lot more options) but beyond all that TurnKey is a customised headless Debian under the hood. So it can be configured via commandline just like any other Debian server.