20-odd years ago when I worked at a facility that handled materials up to SECRET classification, we did much the same thing. It makes sense if you look at it with the right level of paranoia. Bear in mind that such places strongly discourage making unnecessary physical copies of classified information.
If you were working on unclassified material, you used the unclassified hard drive in your computer and the unclassified network cable. To work on classified material, you shut down, pulled the hard drive caddy out, got the classified caddy from your safe and put that in, swapped to the secure network cable, and started your machine up again. (Details are a bit sketchy after this time, but it wouldn't access the network if you started it up with the wrong network cable in place.) On the secure network you had no external network access, if I recall correctly, and no email access (even internal). You were effectively working on a different computer when you were on the secure network.
The overriding principle was that classified information was never exposed to any system that could exfiltrate data. Floppy disks, by policy, carried the security level of the highest security machine they had ever been placed in - it didn't matter if you had only stored unclassified material, if you put it into a secure computer it was now classified SECRET and couldn't be left out, removed from site, etc. [Because secret material might have made its way on there, either with or without your knowledge. When there's a risk of serious espionage attempts, things like worms that might attempt to store data in unallocated sections of a random employee's disk become part of the threat model.]
If you'd used the same OS disk for secret and unclassified uses, who knows what secret material might be left floating around on it when you were in the more vulnerable unclassified space?
Those of us who had mobile phones (I didn't at the time) had a lot of fun rules to comply with in that regard as well. I don't remember those clearly since I didn't have to, but I remember they were absolutely not allowed in any classified meetings, due to the risk of surreptitious concealed transmitters.
Now to be fair, there was a project planned (maybe even started) to investigate whether the secure and unsecure computing environments could be integrated in a safe manner. I have no idea whether that eventually worked out for them. I hadn't heard about any progress before I left that job, but I wouldn't have expected to unles it was almost complete, since I wasn't in the IT department.