Having been in this exact situation at a research institution with expensive equipment and Windows XP only software before - support.
Helpdesk and lower levels of back-end only pay a certain amount so turn over constantly, and “those PCs have had hot glue put in their ethernet jacks and USB ports and burning CDs is the only way to get data out” is a hell of a lot easier to reliably keep going than some esoteric system of VMs and firewall rules.
The people in the lab have way more tolerance for having to burn CDs than they do for firewall changes stuffing up their process and taking a while to figure out and resolve!
Only because I had the same thought and I feel like you might know more, is there an example of software that does this securely?
I see no reason why the data collection can't be managed by a highly portable console app running inside a VM or dos emulator or the legacy PC can't be kept behind a firewall that only lets data out.