I need some lore-minded myst head to explain this to me (but don't mention too much about myst 3 bc im in the middle of it so no spoilers if possible!!!)
In Riven its mentioned that Gehn's understanding of the Art is flawed which is why his ages tend to be unstable and fall apart (Riven being the best example which is due to explode any day) and he's always posed against Atrus who presumably has a much more nuanced understanding of the Art.
My issue is, if you go back to Myst, half of the worlds Atrus creates ending up having odd instabilities. Selenitic starts as a green meadow and lakes, and when he arrives it begins to tremble, and by the end is nothing more than a rocky desert with a small green patch of what once was.
In Channelwood, tremors begin and the forest starts sinking into the water, which begins the history of the floor and tree dwelling peoples.
Either this, or his presence enacts some sort of change that would imply the worlds are not meant to be linked to. In stoneship for example the weather changes to rain for the first time upon Atrus' first arrival. (And less concrete evidence is the death of the last floor-dweller in channelwood changing the multicoloured water to a permanent dark green, although this could've still occurred without Atrus' presence.)
Maybe these are his early ages that he had less of a grasp on being relatively new to the Art? Or maybe the cursed instability that effected Gehn's worlds is something Atrus knows all too well?