Thats the whole point, it was said they made chabges for physical copies and reairing to close the plot hole.

Its a bit over the top but it seems to actually close an ongoing discussion.

That is the point of the video. There were already known differences between the pre-release pilot and the one that actually aired on TV.

So, was the Nibbler-Fry plotline part of the first episode, or was it added later?

Yeah go back and watch older South park episodes and look at how they changed Token's name to Tolkien all to make a joke about Cartman being racist.