There is some indication in soft-canon that the Nebula class was in production before the Galaxy class was ready.
So my theory is the first appearance might possibly be some kind of "block 1" design while the later appearance might be "block 2" and this change was done to ease production since the deflector of both the later Nebulas and the Galaxys would be the same.
As a result Starfleet would only have to produce one type of deflector (and spare parts) for two ships.
[Of course there's also the remote (and totally theroetical) possibility that the original USS Galaxy used the same deflector design as the first Nebulas do.
It wouldn't be the first time the prototype of a new class of ships looked different from the production series and was changed because a different solution was more practical.
Based on that theory the design with the "bulge" was the forerunner of the deflector used on the later Nebula and Galaxy models.
But that is actually just complete speculation on my part.
Would however look interesting IMO. ]
Anyway I agree the original Nebula lower hull design is missing and missed, just like the actual sensor pod from "The Wounded"
I said "Farragut" because that's generally the ship name used to describe that particular variant, like the "Bonchune" is used to describe the later CGI variant.
As to why the CGI version is different, well, when Foundation Imaging visual effects supervisor Rob Bonchune was asked to make a CGI version of the Nebula, he was only given the CGI Galaxy-class built by ILM for Star Trek: Generations as reference to work from. So the ship came out looking more like a hacked up Galaxy than the physical model ever did.