I don't think there's any connection between hand-crafted and linear. That's purely a design decision. You can make hand-crafted environments that aren't at all linear or flat. I've done them myself. Skryim is like that: there are paths through the mountains, stairs, dungeons that open on a low area and exit on a high area, etc. If the landscape forces you along a specific path, that's a conscious design decision the developers made to control your experience. That's not a bad thing, it's just not a consequence of a hand-crafted world.
Not an inevitable one, but a likely one, I think. Morrowind was an example of how one doesn't necessarily involve the other, but in my experience there seems to be a bit of a tendency in that general direction. One could also dispute Gothic 3's "linearity" (or even Risen's), for example, but it shares certain traits IMHO.