I'm using LTN combinator as a smart settings for my non-LTN stations, and it shows me "Not connected to LTN Stop Input" each time I click it. I've checked mod settings multiple times and couldn't find settings to suppress this warning.

This message only shows up if you are out of reach and not connected to an LTN station. You should be seeing both a Can't reach message and a Not Connected message. If you are within reach you won't see them message and it will open the combinator.

You will also see it in map view if not connected to an LTN station. You can only open the combinator via the map or out of reach when connected to LTN stations. Otherwise the reach rule of regular combinators apply. I suppose it wouldn't be out of the question to allow that modification all the time (via setting). I'll probably add that setting in a future release.

I am using the remote configuration mod, so it opens the GUI but displays the messaage. As far as I get, it happens even if I'm within the default range.

Oh, yeah there is some not friendly interaction with that mod that I note in the change log. The author there is supposed to be providing an ability for mods to exclued themself from what remote configuration is doing. I may need to add some additional compatibility there too... It's on my todo list.

Still trying to see if I can make this a better experience... Not forgotten.

Still trying to see if I can make this a better experience... Not forgotten.

You can check if game.player.render_mode equals defines.render_mode.game and show the notification only if it does.
That won't cover all the cases but will definitely cover the most of them.