While it was an interesting twist and revelation, I don't believe the genetic engineering bit was difficult to believe from an audience perspective (to me anyway). He was clearly incredibly intelligent. This was an interesting way to not only give Bashir a bit of a backstory, but also introduce his parents and create some drama/conflict between him and his father, and within himself. It also made for some interesting moments between Bashir and O'Brien as their relationship grew.
But it's not a unique situation for an actor to disagree with writers. Nana didn't like the idea of Kira and Odo getting together at first. She also talked about getting in a screaming match with Ira about a potential affair between Kira and Dukat. Avery said in an interview that he would have done things differently if he was a writer/producer for the show. Rene said he didn't want to do the tux bit before joining the great link in the last episode. I think Terry Farrell said she wanted things to end differently for her character. I'm sure those are just a few examples of plenty of instances over the years when actors battled writers, probably directors as well and more. There are lots of opinionated people who worked on the show and were heavily invested in the characters. Disagreements like that are not surprising.