I doubt that there exists a joint registration. Indeed, one of the biggest pains in bringing aircraft in/out of the country is getting the registrations changed and the confirmation requirements can be a nuisance.
Not having been down to the Museum for yonks I may be a tad out of touch with what Dave et al are up to these days.
However, my guess is that the aircraft is on the Australian Register (ie civil VH-) but has authorisation under the Regs to display other markings. This, no doubt, would require ADF concurrence but I can't see anything to preclude it out of hand.
Part 45 and
AC 45-01(2) refer.