Existe alguma pressuposição de que Bashir foi geneticamente modificado?

Não.

Como indicado na página Memória-Alfa para Bashir na Informação de Segundo Plano :

Making Bashir genetically engineered in "Doctor Bashir, I Presume" was a last-minute decision. As Ira Steven Behr explains, "at the time we were working on "In Purgatory's Shadow" and "By Inferno's Light", we had no idea that Bashir would turn out to be genetically engineered... even though it was the very next episode..."

Alexander Siddig was not happy about this sudden development in his character: "I didn't know about it on Tuesday, and on Thursday the script arrived – we started shooting on Friday. I was so shocked. You know you get the impression that maybe the producers sit down and talk about strategies and character arcs with actors but this thing came out of the blue and pissed me off so royally." Siddig interpreted the change as an attempt to turn his character into Data, a tendency which he fought against by deliberately playing any "Data-esque" lines badly. ref

Esse último bit é interessante. Porque eu sempre achei que quando Bashir estava agindo como um médico geneticamente modificado, suas falas foram dadas de forma simples e pouco convincente.

Não.

De acordo com uma entrevista com o escritor DS9 Jimmy Diggs no Dr. Bashir, presumo .

Já que o episódio a que você está se referindo aconteceu na 4ª temporada, podemos dizer com segurança que a resposta à sua pergunta (estava lá prenunciando antes disso) é um definitivo não. Isso também vale para a maneira em que Bashir foi tratado pelos outros tripulantes que ele encontra.

"Up to this point in the show [Dr. Bashir, I presume], Bashir's background was a big question mark," says [Jimmy] Diggs... "Bashir's background was layered in a fog, which made him incredibly intriguing. So here we had a chance to delve into that background. There was a feeling that he was a very private individual, which meant that it would be interesting to put him into an embarrassing situation."

"I kept saying, 'What's the secret of Bashir's past? What's the thing that this guy, Zimmerman, is going to find that's so interesting?'" says [Ron] Moore. "I remember that Rene and I started talking about genetics, and Rene pointed out that genetic engineering is one of the things that is oddly missing in the Star Trek universe... in Star Trek it's virtually never discussed, aside from the fact that there was this thing called the Eugenics Wars at some point, and Khan came out of it."

"And then Ron just had this bolt of inspiration," says Echevarria. "What if Bashir had been genetically engineered?"