Sorry, I did not realize that was a solder paste deposition machine; I thought it was a pick-and-place machine.
So, it's all "just" a matter of getting the software smart enough and unobtrusive enough that it actually helps rather than hinders the process, compared to doing it manually with no computer assistance/interference. That is an interesting challenge.
Trying to get an idea of what the workflow would be. Say, you want to make a few boards. Do you tip out the components you need from larger containers into, say, a shallow tray with compartments? I suppose you don't put all the passives in one pile, because you couldn't tell the capacitors apart anymore, and even the resistors would be a pain. If they are separated by type in compartments with a geometry known to the software, it shouldn't be too difficult to use a camera to locate the parts, turn them the right side up if needed (requires hardware: TBD), identify the polarity or orientation for the parts where that matters, and position them squarely. The user could then manipulate images of the components over the image of the PCB, with the machine following along and doing it for real, and repeating it automatically for any number of boards.
Again, the key is to make this software easy to use -- not necessarily in the sense that anyone could sit down and use it with no previous knowledge, but in the sense that it would allow a reasonably skilled user to work quickly without unnecessary hassle, and it would try to help while being smart enough to know when it doesn't know what to do. Basically, the user should feel they are working with the machine, not against it or despite it. This brings to mind the cheap sets of screwdriver bits that come with a handle. I have one with a plain handle -- it has a fairly thin stem (considering it takes a 1/4" hexagon), about 2" long, and a plastic handle of a decent size and shape. That is the good one, and I use it often when I need a screwdriver of a kind I don't have as a plain old single-piece type, e.g. hex or Torx (I keep 4mm and 6mm flat, Philips #1 and #2, Pozi #2, and stubby Pozi #1 and #2 to hand). Another set has a ratchet handle. It has no stem but a stubby 3/4" thick mechanism, and the ratchet feature is never useful in practice. Even if locked, the mechanism still has enough give to make the handle very annoying to use; and the shape of the mechanism and handle prevents access in many cases. Instead of a magnet, it has a leaf spring with a ball, and it's much harder to change the bits. That's the bad example, where a "feature" hinders much more than it helps. We don't want that. I always try to aim for the set-of-half-dozen-most-frequently-used-standalone-screwdrivers-plus-plain-screwdriver-handle-with-interchangeable-bits type of software, never the let's-add-a-ratchet-and-charge-a-dollar-more-and-make-it-useless-all-round type.