As I say, we don't yet know how YDL works on PS3. It could be this way, running as an application which is my suspicion and preference. Or it could work by commandeering the hardware absolutely, preventing any GameOS operations while Linux is active and requiring a reboot to return the GameOS to operation.
The hypervisor will not allow any OS to completely commandeer the hardware since it's the boss.
Both GameOS and Linux will run above it and will most likely not be aware of each others existence.
Both may have full access to the hardware but they hypervisor is still in control and can switch between them at will.
The hardware may be virtualised in such a way that gives GameOS priority. e.g. It could be set up so a data BD can be read by Linux but a game or movie BD would not register as being present.