The crew's ability in operating the weather radar is something an investigation would likely look into if that indeed turns out to be a cause, but given the region in which they fly, I'd be disinclined to presume that they were less than competent in operating it.
I fly that area fairly often. Due to the amount of moisture, droplet size or whatever, down low everything can look red and just be rain with little turbulence. And, up at altitude, huge buildups can sometimes paint very little. I often climb not to get above the cells but to get on top of the layers to visually assess the structure of the 'isolated embedded CB's' and their overhangs which can be extensive.
One peek is definitely worth a thousand radar scans on the way to Singapore in my experience. Then, safely on the ground, follow the greens...