That aircraft is now unfit for purpose through no fault of their own. RR could find themselves with a very hefty compensation bill if they don't get this sorted.
It has been interesting to note that since restarting services to LHR with A388, QF have consistently been climbing to lower initial altitude on the LHR-SIN leg than SQ's A380's. IIRC even at MTOW the A380 was supposed to be able to reach initial cruise altitude of FL350, QF been going to FL330 recently from LHR.
Point 1. The requirement for the RR Trent 972 was due more to Airbus delivering the A380 5-6 tonnes over indicated weight, thus requiring the extra thrust. As much or more of an Airbus failure rather than RR, I would suggest.
Point 2. It could be due to different payloads, or as another thought, the g-buffet margins used. At BA, we use 1.3g margins as per CAA requirements, QF may well do the same whereas SQ, I seem to recall use 1.2g margins as per the FAA. That could explain the difference in initial cruise levels. One thing for sure, the engine thrust rating doesn't explain cruise level differences.