The Marker chip at the head of the input bar is the same thing as the one on the image input bar: a picture usually holds several things, and writing "the pillar in that picture" does not tell the model which one you mean — mark it on the picture and it knows. Clicking Marker puts you in Element selection: a bar floats at the top of the canvas reading Element selection and Click an image to select a local element, with Back to node and an × beside it, and the other nodes on the canvas all fade.
Click the spot you mean on an image node that has already rendered. There is a short wait between the click and the result, and the bar's second line reads Detecting… while it runs; once it comes back, a selection box and a name label are drawn on the source image, and clicking that label lets you pick another name and box from the candidates right around it. Clicking something that is not a rendered image (a draft, one still generating, a video node) says Click a generated image node, and a spot nothing can be recognized in says No element recognized here.
A successful mark does two things at once: a marker tag (the source image's thumbnail plus the element's name) is added to the end of the prompt on the input bar, and the image you clicked is wired in as a reference for this video at the same time — the same thing as drawing the line by hand, and it shows up where Using a reference image puts it.
When you send, that tag is not handed to the model as it stands: it opens out in place into a line saying which image and roughly where — the element's name plus its approximate area on that image. The same node expands the same way whether you send it from the canvas or from the command line / an Agent: there is one implementation of this and both render paths go through it.
The two sides are two ends of one operation: delete the tag in the prompt and the box on the source image goes with it; delete the box on the source image and the tag in the prompt goes too. One image can carry several marks, one tag per spot.