His body isn't inherently durable (compared to most of the monsters and enemies he fights), he has really good regeneration abilities. Think of it like Deadpool, you can deal damage to him, but it doesn't tend to stick.
No, I don't think so! On the contrary, I strongly disagree with your comment! MC's body has always been strong, it has always shown excellent potential. Look at MC's fight against the monstrous Kenny in the Frat House Massacre arc. MC was able to go toe to toe with the monstrous Kenny even at level one, and with very few trainings! And in the fight against the birb knight "Valravn" in the hero arc. MC was still at level two, and he was able to go toe to toe with Valravn even though he was weakened. I mean, MC's regeneration, is one of the most strong and powerfull things in this game and makes him the most durable in physical combat compared to other superhumans.
The problem here is this forced script, which prevents MC's potential from growing too much, so that the story develops the way it wants. After all, the dev doesn't want an Ella 2 running wild! Let's remember that Ella, level 4, gave trouble to Hero Captains like Clark and Alexis, who were level 5.
Anyway, concluding here, I think that in a physical fight against MC and his regeneration, if the enemy doesn't use persistent damage, such as being set on fire, poisoned or soaked in acid, there is no way for MC to lose, unless the script makes him lose in the silliest way possible.