I'm sure the dwarves can handle schlepping stuff around on foot. However, even though I haven't been at that point to do it myself, I think training those extra dwarves for military and setting up fancy patrol routes everywhere, or at least using them on rotation with your other squads to give those more time to train/drink/party, is a better use for them. Or building a 20-storey palace out of glass blocks.
I'm also doing this for interest/challenge. I wanted to play with minecart logic. And I'm always fascinated by what strange things you can push a game's mechanics to accomplish. Plus they're dwarves. They mine. They use mine carts. Mine carts are available. There's a magnetism to use them however possible.
As for adapting layout, normally you'd have to have tracks crisscrossing around for each route. Without careful planning before digging the level, you're either negotiating real-estate or weaving tracks all over the place. Detours around entire blocks of rooms, up and down z-levels, etc. There are probably ways to do multi-route tracks without computerizing it, but I can't think of how.
With what I'm working on you can connect 4 or 8 or 20 rooms together with a single straight track which leads right to a central hub. Run a ring around the perimeter of your workshop's level, use about 6 tiles of any room/section you want to to distribute to, and you're set. The only hard parts are the control room design and connecting all the gears and pressure plates.
Hmmm. I just thought of something. A binary splitter could cut the number of controls in half! Madness.