You might want to read the Volume and Mass thread: http://www.bay12forums.com/smf/index.php?topic=61215.0
That thread is basically all about using metric units rather than arbitrary abstract units.
I'm more concerned with the production side of things than trying to quantify the space in a square (I think the latter is important but it's more grandiose than what I have in mind).
I like this idea, but how would the game display the parts of the boulder/bar/log that aren't used up? The cloth rework handled this by permanently locking the cloth in a hospital chest. Perhaps one could give workshops the same sort of storage.
What I would probably come up with is make a few base "types" of items, eg "large boulder" "small boulder" "rocks" etc then any "leftovers" could be stored in the workshop in a similar fashion to how melted objects are now.
So using the numbers above if you were making a stone hatch that requires 6500 stone from a 10000 stone boulder it would produce the hatch, 3 "rocks" worth 1000 each and leave 500 stone "points" in the workshop for future use.
The "rocks" might be used for mugs or rings or other crafts while the "points" could be used towards extra requirements on other projects.
If there were a particular need to make things into a transportable object I could see a units made into dwarven concrete, wood crafted into boards, and metal forged back into bars.
A more complicated method would be to just keep track of the "value" of every boulder/bar/etc, but I think that would end up just making more of a mess in the fortress (not to mention I'm sure my ever-loving stone craftdwarf would carve a single ring out of every boulder just to spam me with cancellations).