I think scalability would be a key factor. You could make the machines 3x3x3 or 10x10x10, or anything in between, it would accomplish the same task, but the speed of the process, and the amount of fuel required to run it, would be different. A huge, house-sized blast furnace with an accordingly big air supply fan would spit out steel at a rate of stacks per minute, whereas a humble, fits-in-your-basement model would process an ingot every now and then. The upside with the little version is that it would require less fuel and startup time, whereas the big one would need a dedicated tree farm/charcoal smeltery, and run for days before reaching its final temperature. Heating components and insulation could be added to speed up the process or reduce the cooldown rate. I also suggest that fuel would only be used to raise/maintain temperature, and the processing time would be affected by temperature only, not fuel input (though fuel affects temperature, so there is a link).
The problem with multiblocks, though, will always be that they are resource demanding. At all times, the game needs to check for completed structures, and when hundreds of blocks work together to form a structure (of which your base might contain a few), your processor might be tempted to ragequit and crash the game.
A possible approach to this problem would be doing it bed-style. The Vanilla bed takes up two blocks of space, yet is placed and picked up as a single block. It would possibly reduce lag, but leave out a lot of flexibility. Custom incineration chambers would be out of the picture. There would also be a question of how to assemble it. Would you combine its components in the GUI of an assembly block? Build the thing on a huge construction pad (a flat multiblock in the traditional sense), where it drops as an item after completion? Or something else entirely?
Either way, I look forward to seeing how you'll handle it. Best of wishes!
