USB – Can Thunderbolt 1/2 Devices Connect to Thunderbolt 3 Adapter?

Yes, that will work just fine. Notice that the female DVI connector has more slots than the male connector has pins. Those slots are for the extra pins needed by a dual link cable. They're not needed for a single link DVI connection, so they'll just sit unused.

After more playing around, I now have a workaround whereby using a Mini DisplayPort to VGA adapter instead of one of the Mini DisplayPort to DVI adapters, i.e. an analogue connection to one of the displays instead of digital, seems to work and allows me to have 3 active displays configured like so:

Display 1 connected via HDMI to DVI adapter (into HDMI port)

Display 2 connected via (passive) Mini DisplayPort to DVI adapter into Thunderbolt port 5 (as in the diagram in the above article)

Display 3 connected via Mini DisplayPort to VGA adapter into Thunderbolt port 2.

However, I was hoping to have an all-digital solution as the above Apple article suggests I can, so I'm still hoping someone will come up with a better idea!

UPDATE: This appears to be an issue introduced with OS X 10.9.3. Tried an identical machine running 10.9.2 and the second configuration I tried in the original question worked just fine. Hopefully it'll be fixed in 10.9.4, until then the workaround above is still valid.