The higher altitudes put them closer to both their stall speed and overspeed mach number, a.k.a. puts them into a "coffin corner".
Smaller airpeed margin, less room for error in turbulence.
CNN weather guy was showing map and stating the turbulence and storm went upwards of 53,000 ft, so no way to avoid it.
The Sunday Shelf was all above sea level during the last Ice Age and the Java Sea averages 150 feet deep so this should bode well for the recovery effort.