Protected against what?
Far more concerning from a RISKS point of view is the spare parts being physically in the same place as the live machine.
What other program? Most DOS versions were not multi-tasking beyond "terminate-and-stay-resident" (TSR) programs like mouse drivers.
Whatever application you ran on DOS was THE application your computer was running.
Top parent of this thread is talking about a package for AmigaOS being run on a bespoke emulator (as the Unusable Amiga Emulator of the 90s wasn’t really a thing that could be used for that)