It's hard to tell if the flags are actually covered in all but the last picture, and even then it's still kind of hard to tell due to the angles at work in the photos. The emphasis seems to be on one flag in particular.
The first photo has said flag appearing to be left of the siege shield at the top right of the frame, next to a small green bush on the right and a darker green bush on the left Whether or not it looks like it is under the tower is inconclusive from the angle given. There's a dead Destrier in the background of it and the distance from the flag to the wood pile looks a lot different compared to the next photo.
The second photo gives us another understanding of where the flag is in relation to the landmarks from under the tower (the wood pile, the bushes, the dead Destrier) and it appears if we can see the top of the flag imposed over the bottom "lip" of the tower from this angle upon zooming in 300-500%. It definitely looks like the flag is outside of the tower if only by a thin margin.
The third photo gives us yet another perspective. We can see the siege shield from the other photos in the left half, and the bushes as well. The flag definitely appears to be under the tower. So we have one inconclusive photo, one photo where it looks like it's over the lip of the tower, and one where it looks like it's definitely under there. Hardly leaves us with anything solid, really need a video to say for certain.
In any case it's plainly visible- if it is indeed under the tower (which has been left unclear) it's right on the edge and should still be able to be put down via the F key. AFAIK the siege tower doesn't actually disable the flag from working; spawns can still be set at even flags completely covered beyond sight- I know from having done it before- so it stands to reason that it can still be disabled like any other flag; this, of course may be an erroneous assumption on my part, but it would also be quite hard to disprove as the issue may be that the siege tower could be holding people within it which are included within the detection radius of the flag, thereby disallowing the disabling of said flag.