What is the meaning of the three dots in The Beginner's Guide?
My Research
I had a quick look around and it seems as though no one has really come up with a definitive answer.
It's all just speculations on forums and discussions about the game.
The creator of the game hasn't made a statement on the dots.
An idea that someone had:
https://steamcommunity.com/app/303210/discussions/0/490121928348490895/
My Idea
To me it looks like the developer added the dots in almost just to mess with people. See how far they would go to try and analyse and figure out what it all means but in actuality, its just 3 dots on a wall.
Summary
There is no answer to your question, the dots are up for interpretation from each individual player.