It might be that my problem is related/identical to an issue reported on the Tutorial's github repository, where a user reports that his character doesn't move. Just sayin'.
It is well tutorial with a lot of insight. But now I got a new problem, I am sorry @TwistedTwigleg .
I reached the end of part 2 and started with part 3. At the start, two scenes are introduced, space and ruins. They have nodes for ceiling/floor/walls, but at least the floor doesn't "hold", the player and other bodies like cubes fall through. There are a bunch warnings (e.g.: "return value discarded" and "unused argument", probably just cosmetics I suppose) but also errors of type "rocover from penetration" in Player.gd in function process_movement, the line
vel = move_and_slide(vel, Vector3(0, 1, 0), 0.05, 4, deg2rad(MAX_SLOPE_ANGLE))
Edit: ok, I found out that assigning the mesh library Space_Level_Mesh_Lib.tres to the floor_and_cailing node fixed the fall through for the player. Doing the same for the Walls fixes the rest, also the bounciness. The level plays nicely, then. So I think that fixes the issue, and the errors have disappeared. I love it when errors disappear :-)
Nice level. I like the atmosphere :-)
Cheers