I have mastered all three languages, and quite a few atlas... for a total of 1,004 words.
I can confirm that once languages are learned you do not pick up the atlas language. Even after the most recent patch. Only way I have found to get atlas words is via monoliths.
However since the patch, I have not seen any of orange light beacons on any stops on 5 planets, and have only come across 1 or 2 monoliths in that time.
As for the gates/portals, I have tested it a little, though not extensively, and it appears that if you follow the monoliths, then you get to a portal. Whichever way the blue light from the stones are facing, go that direction.
Unsure if that works since update though.