I have been trying to make personal markers on the map so that I can remember the spawn points for various plants and such (do mining points respawn in the same place), but there doesn't appear to be a way to make your own waypoints. You can put a marker on a map point that's already discovered or a large town, etc, but there doesn't appear to be a way to make one at your current position. I would think, given the size of the map and the relative complexity of the game, that we would be able to make our own map waypoints, label them, and give them a brief description.

Is this functionality already in the game and I'm just missing it?

I don't think so. This feature was even in Arena.

You can place a single custom destination, but it's messed up so you can't place it too close to the little arrow that signifies your characters current position on the map.

that would be awesome because i would hunt down and mark everything in the game lol but no they dont have the feature which svcks but o well i guess