Although I understand that the pilots should have aborted way before I'm not too sure to understand as why they hit so hard ? When you have a 1100 ft/m sinkrate why on earth would you add a pitch down command ?
Keep in mind that their GS was about 190kts, so their sink rate to maintain a 3 degree slope is close to 1000fpm. It does not take much to turn 1000fpm into 1100fpm. Especially when you are flying in bad weather in the mountains.
The combination of high elevation and high ground speed means your margin of error is much reduced. And I believe that SEQU's GS does not bring you to the ground, so there you have another threat which contributed.
As far as hitting the ground so hard, you have to take into account inertia. I'm not a bus pilot, but in the 747, when you get close enough to the ground, you run out of room to correct your sink rate. So if you incorrectly push slightly down passing 200' agl to correct for being slightly high, you have pretty much sealed your fate to a hard landing. I suspect the A346 is probably similar in this regard.
This height is also increased if you are flying a steeper than 3 degree slope, which these guys probably were doing. The control inputs this guy used probably worked ok down low, but they didn't up at 9000 feet.