Better question is, is doing maintenance in DXB better then doing it in MNL.
Qantas contracted with Emirates Engineering to repaint 8 A380s and replace 1 set of landing gear. It isn't confirmed if they are also doing heavy maintenance checks.
Thus far, Qantas has used Lufthansa Technik in MNL to do their C and D checks, which has normally required a SYD-MNL positioning flight (however some positioning flights have been HKG-MNL, and a handful of checks at the start of the contract were done in FRA with positioning flights to/from LHR)
Qantas signed a 10 year maintenance contract with Lufthansa Technik for the A380s, but it isn't clear when this contract started. There are varying dates on the news stories about it. The stories about Lufthansa Technik are dated 2012 and 2015, but the first QF A380 went to Lufthansa in 2010...