Ah good point, I thought that you had to walk around the bounded area, but you're right, the Boundary description doesn't seem to require it and the Aegis description only says that this is often done, not that it's a necessary element of the ritual.
The boundary description does not necessitate walking the boundary, but the description of the aegis does (it is a somewhat non-hermetic spell). However keeping a stone building surrounding the covenant free of water is a simple question of elevation= if the first floor is raised above the water level (perhaps filled with loose rocks and sand beneath) then you should have a dry walkway. Unless of course there are supernatural properties to this swamp...
AM5: "The entire covenant usually participates in the Aegis ritual, which often ends with the participants walking around the perimeter of the protected area in order to define it."
Notice that often does not equal "always" or "must". It seems to be an optional element in the ritual, much like casting it on the winter solstice is a tradition, not a requirement.
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The other thought is that if it ends with them walking the perimeter the ritual could begin before sunrise and end afterwards.
As mentioned earlier, we can't venture outside whilst the sun is down.
Which means you could a) build a structure around the covenant b) emerge right after sunrise for the march around the covenant, or c) ignore the tradition and hope the SG doesn't decide it comes back to haunt you.