Ah, yes, excellent point. I think this will work.
In my early tests, the PNG frame export brought a SAS RAID 0 array to its knees, but if I partition as you suggest, I can easily save 200000 frames to a ramdisk (the render machines have 32GB).
As a bonus, I pretty much get a distributed solution for free. I can chunk and distribute the (small) data file across the render farm, have each machine render 200k frames at a time and send back the small mkv, and then trivially cat the result on the master.
So, it's actually a good thing you posted twice, because I can give you two richly deserved upvotes. :-)