Unfortunately, the Long Haul EA does not specify that a pilot can be only be stood down for a 'total' "stoppage of work". The words in clause 15.6 refer to a 'strike, stoppage or other limitation of work for which the company cannot be held responsible'. A 'limitation' does not require all work to cease. Moreover, the stand down can apply to individual pilots, it does not have to apply to all pilots, or an entire category of pilots; note the use of the words 'an Australian based pilot' and 'the pilot'. So a limitation that only affects the work for a handful of employees can result in partial stand downs of a group of pilots.
Regarding running a RIN and then Qantas carrying the surplus, this is an important point. While the RIN process is specified in the Agreement, it does not state that he Company has to conduct a RIN. The 'right thing' to do for pilots might be to RIN A380 pilots to other long haul types that are flying. However, if there is cost involved, there may be pressure from within the business to carry the surplus on the A380 and not RIN anyone. If you were a cynic, you might conclude that Qantas may be motivated to talk about A380s coming back into service as it affects the ability to stand down pilots on that type.