Possibly relevant to the eternal "how much was planned in advance" question. Here's a list of things in the comic that, in retrospect, are consistent with (and therefore potential clues to) Megan and Cueball climbing out of a deep basin with a central salt lake.
Most of them aren't strong clues because they have other plausible explanations, including being art production limitations (e.g. not showing plants moving in the wind every frame). But still...
- Lack of waves and tide on the sea, also suggesting lack of wind.
- The sea has risen and fallen before (but not this fast). Without tides, why would it rise and fall at all? A salt lake rises and falls gradually as evaporation overtakes inflow and vice versa.
- The barrenness of the land near the sea, even at the river delta and right along the fresh-water river upstream. This is highly unusual, as I commented on at the time. The cause would most likely be salty soil from relatively recent rises and falls of the salt lake.
- The bad/salty taste of the water. Of course, normal sea water tastes bad too, but Megan's reactions to getting some in her mouth, in retrospect at least, does seem exaggerated compared to how someone familiar with normal sea water would react to getting a mouthful of normal sea water.
- It gets cooler and windier as they climb. Of course, this would be true just about anywhere, so it's hardly a clue, but it's consistent.
- Despite getting cooler and windier and the air seeming thinner (suggesting at least a couple thousand meters of elevation), it never became noticeably windy or uncomfortably cold, even at night. I commented on the strangeness of this several times (as possibly suggesting massive climate warming) especially after it became clear that they weren't at a tropical latitude. Starting in a basin explains it.
- Cuegan's reluctance to attempt to swim in fresh water. Swimmers are a little more buoyant in normal ocean water than in fresh water. The difference is noticeable, but it's not big enough to completely alter basic swimming and floating techniques. If you can swim safely in an ocean, you can almost certainly do so in a river (barring fast current, piranhas, etc.). Salt lake water, though, is very different, allowing people to float safely with no swimming technique at all. "It's extremely dangerous to try to swim in rivers" is a reasonable conclusion for them to have drawn from their likely past experiences with their sea and with their own river.
- The shapes of the land during their ascent. Basically, a series of broad stair-step plateaus at elevations in between the salt lake sea level and the "coastal" plateau at the first survey tower. This is not typical of most hill and mountain landscapes, where even low peaks have peaks. It was hard to tell this for sure from the more or less 2-D views (a plateau might look the same as a flat section of ridge) but in retrospect, things like the vineyard make more sense on wide stair-step plateaus than on some sort of col or ridge line.
- The shape of the ground on the slopes they climbed. There was lot of soil cover and not much exposed rock, compared with most mountain slopes I've seen, including very old eroded mountains like the Appalachians. Soil formation on mountains is slow and it erodes downward; there's almost always less soil farther up. In a basin (whether underwater or exposed), sediment drifts down and washes down from a wide region above.
- The "pretty crumbly" and sandy-looking rocks Cueball noted at the wowterfall. Real sandstone isn't all that crumbly, but compacted sandy sediment might still seem stone-like but erode quickly. At the time, we thought Cueball was overstating how crumbly the rock had to be for the water to cut through it, because he was unaware of geological time scales. But it turns out the wowterfall landscape really wasn't formed in geological time scales, but in a few millennia at most.
Was it possible to figure out the setting from these clues (along with the astronomical information) as a puzzle? Some people did make correct or nearly correct (e.g. the Black Sea) guesses, but no one put all the above bits and pieces together to make a strong case for the Mediterranean basin. I think it might have been solvable, but you'd have to make some fortunate assumptions about things like which of Megan and Cueball's observations are accurate (e.g. how crumbly the surrounding rocks appear from a distance) and which features of the comic images are literal and which are art conventions.