Looking at the video of the removal of the aircraft, it appears that the nose gear is not fully retracted (or extended for that matter). I know that aircraft with gear doors on the main gear suffer from increased drag during the gear cycle, so perhaps they were climbing when the gear was selected up & the extra drag, coupled with other factors, caused it to lose altitude & settle back onto the runway.
If the PF was increasing attitude in order to try & prevent the altitude loss, the aircraft may have struck tail first, explaining the damage to the underside of the rear fuselage. The aircraft would then rapidly pitch nose down. If the right wing was slightly down, then most of this force would be brought to bear on the right engine nacelle & may have exceeded the design strength of the engine mounts & pylon, causing the right engine to separate, different to what happened with the BA & LOT crashes.
Lots of speculation. The final report, if we ever get to see it, will make for interesting reading.