So, was Daniel Craig's accent part of the Knives Out script?

Sort of. From an interview with Rian Johnson:

Sims: I hope the answer is no, but was there ever a point at which you said his southern accent was too much?

Johnson: No, though I’m sure my producer was sweating. Jamie Lee Curtis reminded me recently that in the script I described [Benoit Blanc’s] accent as “the gentlest southern lilt possible.” But when we got on set, I was just having so much fun watching [Craig]. I think in the movie, it probably takes a few minutes to adjust to him having that voice, but I could listen to him forever.