The Stage 2 only applies to the small number of staff who are in essentially holdover jobs - e.g. their post was lifed or has been scrapped but they are staying in. Anyone coming back from an Operational Tour will usually find themselves in this spot too. This gives them a small window to apply for posts, but after a finite time they too face being booted out.
No different to the military where sometimes people find themselves out of a posting for a short time.
Its nothing to do with the redundancy process, which has seen tens of thousands of MOD CS laid off in the last 3 years.