Mah, personally Indominus had show better durability compare with Kong.
Indominus was show that gunfire had no effect to her, she had took the tail of an Ankylosaurus in her face without damage, she even took multiple bites of the T-Rex in the neck and even took the bite of a much bigger Mosasaurus and still survive, before be drowned by the latter.
Kong was maybe able to took Browning Machine Guns, but the damage that had suffer was lethal and he was never be directly hit by the Artillery (like the I-Rex never directly took by the AT4 Rocket Launcher). Also the type of bullets that kong had took were .30-06 Springfield, that are smaller than .50 Caliber.
Indominus 's bite and claws are going to hurt a lot, as both were able to destroy the Gyrosphere, which was made by bulletproof glass, able to stop a 50. Caliber Bullet (and if you see the scene, even the muscles of her Jaw was damage the Gyrosphere).
While both are most likely in the same tier of speed, Indominus is smaller so she had more possibility to outmaneuver Kong in the fight, especially when she had the DNA of a Raptor. And Kong could be bigger, but that advantage is not that massive, not when the I-Rex had kill a herd of Apatosaurus, that are bigger than Kong.
"I mean, she had a tough time taking on a T-Rex and a small raptor, but Kong managed to take down three V-Rexes who are bigger, stronger and mroe durable than your average t-rex"
Look that Indominus was winning with ease, only the intervention of Blue had save the day and give to Rexy the opportunity of strike back, while the I-Rex was distracted. And even after that, Indominus was still enough right to continue to fight and could have gone either way, without the Mosasaurus.
And Yes, Kong was able to defeat the V-Rexes, but you now take out of context the fight:
He held off 3 for a few moments, during which time 1 of them tried to attack him twice, most of the time they ignored him and focus insted to Ann. Even Kong had never had time to actually land any serious hits, other than the one with the boulder, and he spent entire time just knocking them back while they just didn't do much in the way of fighting him. Then he and two of them fell off a cliff and were caught by a bunch of vines. In that scenario Kong has a massive advantage given his simian form. Then when he hit the ground, he properly fought ONE of them, and killed it after a struggle.
If Kong was fight all the V-Rexes without Ann and in a neutral battlefield, i doubt that Kong was gonna win without at least be damaged a lot.