Which F1-score is used for the semantic segmentation tasks?
I looked very quickly and only at the first paper so I might miss something but it looks to me like the task is a binary classification problem. If this is correct then there's no need for averaging the F1-score.
Also in this paper the authors even give the formula of the F1-score (!), so I'd say that they are quite thorough in their description of the evaluation measures they use. I would take this as an additional indication that there's no averaging,  since it's unlikely that they wouldn't mention it.