How many floors do you usually wind up with in a decentralized layout? I'm hesitant to push them too far in any direction, and how big you make your rooms would also be a concern (dormitories and 1x1 beds without walls easier to fit around your industry). It sounds like Toady is close to making the next release, so I'll experiment with broader, decentralized forts after that.
Since I can plug 4 workshops around a single stairwell, I can make arbitrarily many stairwells, and I tend to use the maximum populations to throttle immigration to waves of a relatively manageable 10 at a time (changing init settings to increment up 10 every year), I generally get by needing one floor of workshops unless I go on long enough to need maybe 2 floors at most. Keep in mind, I don't need to have only one staircase, either. For my smelters, which I keep on one floor just because channeling magma into multiple floors is more hassle than it's worth, I use multiple stairwells up to different floors. My glass furnaces are just built around the point where minecarts drop sandbags and accepts sandbags back before being given the push to go back up. This is on the same floor as, but fed around a different stockpile (actually on the floor above) the metal smelters.
That said, workshops are not always on the same floors, spread out evenly. My latest stone hub, for example, had a boulder depot for collecting stones and a mason that cut boulders to blocks, then shoved them into a minecart that pushed it down a floor into the actual quantum stockpile of blocks, around which the main masonry workshops (and stone craftsdwarf workshop) were arrayed. I then shoved output from that into a minecart that took a one-tile trip to another hole to a finished goods quantum stockpile. Even six workshops were too many. By contrast, the food production was up one Z below the surface in the soil in the center, directly above the dining hall with the food stockpiles on the floor between. The dining hall had 7 stairwells upwards for access to the food and booze stockpiles, and those stairwells also went downwards to access the residences. The standard dwarf's room was 4 to 6 tiles, arranged in roughly hexagonal pods of six. I assign larger rooms to married dwarves who share the room (and give them an extra bed, besides).
I was challenging myself to use only ramps, not stairwells for my "main" fortress, (the up/down stair you can see is for an aquifer-to-cavern "chicken run", and not part of the "real" fortress) incidentally. I was experimenting with the style to accommodate that, and chose at least 4 rather than 3 mid-game, so pardon the asymmetry.
In that fortress, the connections are through the corners of the quite large dining hall, and at the bottom of the residential stack, although it's worth again noting my fortress is also decentralized by height. Using ramps, the deeper industries are also slightly further either North or East than higher-up industries. (You can see two of the ramps on the Northeast and Northwest edges, although no workshops are on that particular floor.)
My smelters, for example, were lower-down, because I wanted to keep the magma channels I flooded away from most of the other industries. This included a sandbag dropper I mentioned previously that had to go through an aquifer, which was a bit of an engineering feat in itself. Wood and cloth were similarly tossed down a hole to reach a mid-level crafting zone, although I merely required a hole for those, not a returning minecart to carry empty bags back up.