In this instance the keeper was coming out to try and block the ball not the 'space'. But Jota mis-controlled the ball and sent it in another direction completely. Rather than chase the escaping ball Jota continued his run towards the keeper.
All of his momentum is taking him towards the goal and away from the ball, so in order to change direction he has to be able to place his leg further to the right to be able to push off it. You say that he 'continued his run towards the keeper' but it was literally two steps in maybe half a second. People (mainly pundits) make it seem that he changed direction from towards the ball to towards the keeper, but that was already his natural direction and he was trying to push off to change direction towards the ball IMO.
Also, if you deliberately change direction to initiate contact from a 6 foot 3 inch GK who weighs probably 14 stone and is sliding towards you at pace, don't you think it would be a natural instinctive reaction to raise your arms to deflect the impact and protect yourself?
I also don't see why the fact that he mis-hits/ mis-controls the ball has any impact on the decision? The keeper has gambled everything on blocking the shot, as he knows that as long as he makes contact with the ball then it can't be a foul (unless it is studs up, high, or reckless). Ironically if Jota gets the touch that he actually wants then the keeper probably saves it as he is close enough that getting the ball over him would have been very tough. But he doesn't and the ball rolls to a position where it is still in play and where Jota can still reach it, so now the keeper is in trouble because he can't avoid the contact and can't get a touch on the ball. It's always been the case that if the striker gets to the ball first and the keeper makes contact that it is a penalty, even if the touch from the striker is away from goal and even if it is heavy and likely to run out of play.