Depends on both the "regional flavor" and to some extent the whim of the designers. The large 19th century Cavaille-Coll instrument in Saint Sulpice Paris has 5 keyboards, and these are used in a somewhat unusual way, but quite logical given the time and the region. Most C-C organs separated each division into "foundations" (Fonds -- flutes, diapasons, strings, and soft reeds) and "loudations" (Anches -- loud reeds, mixtures, mutations, etc.) and these were on separate chests with separate wind supplies. There would be a foot lever that could turn on or off the wind -- called a "ventil" -- in the Anches chest. This would allow a loud-adjunct combination to be set up on the Anches chest and brought on by turning on the wind.
The organs from that period did have touch assists (done by pneumatic amplifiers called "Barker Levers") but they didn't have stop combination memories or crescendo pedals, etc. So the ventil levers were useful.
Also, the Barker levers made coupling really useful. The order of manuals in these organs from the bottom is Grand-Orgue (Great), Positive (Choir), Recit (Swell), and they are often played all coupled together -- and this allows going from loud to softer to softer by moving up the manuals, and vice versa.
A fourth manual is usually call "solo" and it is usually the topmost.
"Full Organ" is called "Grand-Choeur" and it is most everything with everything coupled.
Cavaille Coll got the idea for this large organ of its time (100 stops, now 102), to have two keyboards for the Great manual, and at the bottom of the stack: have the "Anches" for the Great be on the bottom manual, and the Fonds for the Great be on the second manual, and have them usually coupled together. This is very handy, and allows rapid easy contrasts. The bottom keyboard is called the Grand-Choeur not just because it is loud, but because it is often the case that all 5 keyboards are coupled together, so that one gets both different colors and loudness on each, but so that one can move down to get full organ.
To make this work, one still needs to control the pedal loudness and timbres, and again a lot is done with both coupling and ventils.
The order from the bottom is Pedal, Grand-Choeur, Grand Orgue, Postive, Recit, Solo.
The other important detail about this large organ is that it uses quite a few ranks of pipes from the previous baroque organ, and these are generally softer. So the build up of sound on the Saint Sulpice instrument is done by using a lot of stops, and the voicing is quite marvelous to allow a very clear sound rather than just mud. One of the most thrilling sounds on any organ is "all the flutes" on all the manuals coupled together and played separately and together.
The current main organist at Saint Sulpice is Daniel Roth, and besides pieces played by him on YouTube, you can also find "Daniel Roth demo" clips of him showing how the instrument is organized.