It could be a situation similar to the USS Constellation (1854). The Enterprise is intended to be the original ship (more or less) but is in fact very different. I'd prefer to think more of the original was kept than in the building of the Constellation in 1854, but whatever they did, it changed the ship considerably.
IMO that makes no sense. What does make sense was this was a normal refit and she always looked like this, and they were just upgrading the electronics and such on a 20 year old ship after a long mission. I honestly think that was the intent at the time.