Originally Posted by
tdb
I have a feeling you are interpreting the latter part as an independent sentence, when in reality the "Stand where" applies to both the first and the second parts. Adding some more words: "Stand where the birds are opposite your debuff, and also where the portals behind you and to your side are of different colors." Or putting it another way: "Stand where the birds are opposite your debuff, and at an intersection of two different-colored portals."
Explanation, which you probably already know: Portals of the same color are linked. If white birds go into the red portal at the back, then white birds will come out of red portals at the side. Red = white, blue = black (in this example). You want to get hit by different colors. Thus if you have the dark debuff to begin with, you want to stand in front of the red portal (where white birds go in) and with a blue portal to your side (where black birds come out).
Further explanation: The portals and their intersections form a checkerboard pattern of alternating safe and lethal squares. The initial positions of the birds make two entire columns lethal. Thus there will be four safe squares on the playfield. This is somewhat similar to the grid mechanic on the first boss of Orbonne Monastery.
Edit: The goal of this sort of short instructions is to give players who do not grasp the logic of the mechanic something to memorize. Those who do grasp the logic will sooner or later come up with their own way of figuring out the safe spots from the clues, as you have done. But given how impatient people are it's impossible to teach the full logic to people after entering the instance.