Yes, it’s a bit tricky work-around but you can remove them on PC too, just with mouse.
Click and HOLD RMB on the marker you want to delete.
Now click and HOLD LMB too.
Now release RMB.
What you should see now is the marker box filled out with your custom marker’s name. But when you try to move the pointer to it, the map has gone all weird with scrolling.
Don’t despair, just alt-tab out of the game and then back in, and you’ll see the scrolling stops.
Then click the / - icon so the OK button changes to “Delete”, and then click Delete.
Bit of a hassle, but at least lets you remove custom map markers.