To add to Cos's reply:
Terrain tile layout: Starting setup. This is described in the official rules, which are available from
this link as a PDF. See "Illustration A" on page 3.
Terrain tile layout: Variable setup [with default numbers]. The 18 resource hexes and the desert hex are placed completely by chance, then the numbers are placed according to a fixed formula. Starting at the northwest vertex of the board and then proceeding in a counterclockwise spiral, the numbers are placed on the hexes in
this sequence: 5, 2, 6, 3, 8, 10, 9, 12, 11, 4, 8, 10, 9, 4, 5, 6, 3, 11 (but skipping the desert). For example, the western vertex is a 6
unless the desert is one of the three hexes on the northwest edge, in which case the 6 will appear on the middle hex of the southwest edge. Crucially, this setup will have a 5-6-9 intersection if and only if the desert hex is on one of the northwest, southwest, or south edges. The centre hex is an 11 (unless it is the desert). Hexes with the same number never border each other, and generally are far away from each other.
Terrain tile layout: Variable setup with random numbers. The 18 resource hexes and the desert hex are placed completely by chance, then the numbers are also placed randomly with the one proviso that a 6 or 8 may not touch a 6 or 8. The northwest vertex is not necessarily a 5; it could be any of the numbers. (Although there are still one each of 2 and 12, and two each of 3 through 6 and 8 through 11, for a total of 18 numbers.) With this option selected, it's possible to have two very-high-production intersections, for example an 8-5-5 in one place and a 6-9-9 somewhere else, but there can never be a 6-6-4 or 6-8-11, for example. That's my understanding.
Terrain tile layout: Monthly setup: "Layout and numbers randomly fixed for the current month". I'm kind of curious how BGA decided to offer this option. It might be interesting to play the same board setup a few different times, with different players. You could see in one game, what choices of first-two-settlements turned out to be most advantageous, and then you could choose those in your next game.
Harbor layout: This menu appears if and only if Terrain Tile Layout is set to "Variable setup" or "Variable setup with random numbers".
Harbor layout: Default setup. The same harbors (maritime ports) appear in the same position every game; for example, the wheat port is always on the north edge; the brick port is always on the southwest edge, there's always two 3:1 ports on the south edge.
Harbor layout: Shuffle frame pieces. I'm not sure about this one.
Harbor layout: Shuffle harbor pieces. There are still five 2:1 ports (one for each resource) and four 3:1 ports, but each appears in a different place each time. For example, instead of always being on the north edge, the wheat port might show up on the southwest vertex. But there is always some harbour in the same position as a harbour on the default setup; for example, there is one harbour on the east vertex, with both its docks touching that single hex, while on the west vertex there are two harbours, each touching that hex and a neighbouring one.
Combined trade/build phase. This is set up as a menu but as far as I can tell it can only be set to "Enabled". Maybe originally it was intended that the table administrator could either enable or disable that option, but the way the game is actually presented on this site, it is not really an option at all because it is always set to "Enabled".
It would be great if the developers, Darhf and Lordalx, could chime in on this thread to correct any errors I may have made above, and also to explain what the difference is, practically, between the "Shuffle frame pieces" option and "Shuffle harbor pieces".
