Well, You're right about the base defense (though I'm really looking forward to see my "antfarm" in Battlescape ^^), but this is an issue which already haunts me in industrial tileset missions.
Since i started playing xenonauts with the actual build (on steam ^^), I didn't know about the "highlighting" when clicking on the "Alien contact" symbol. I saw the camera center on the alien's location, but it doesn't paint the enemy in any way (acceptable on day missions, very annoying on night missions ^^).
Maybe I just need to get the hang of it, I'll keep my mouth shut about this issue unless I'm not a base defense virgin anymore and the next build is rolled out, so that aliens might get highlighted properly.
Thanks for providing your answer by the way.