Whether you see a trait as a positive or a negative does not mean it is useful to anyone to ascribe gendered terms to it.

A female software engineer who does not strive for beauty in code, is she less feminine? A male software engineer who strives for code beauty more feminine than the female one?

It is a useless argument to get into, when the actual way to describe the type of code would be a choice of "beautiful, sorted, structured, consistent" instead.

Gender, as such, has nothing to do with it.

Not at all, I'm just wary of reinforcing gender stereotypes.

Even in the conclusion quoted here, the author says "I think it's quite a compliment". As if when you first hear the term "girl code", you're supposed to think "ew", and the author is there to convince you otherwise.

Why not just call it neat or organised instead? Using a gendered term does nothing but appeal to stereotypes and solidify them.

It's a prejudice about the human doing the work. It's not complicated to understand what the problem is. You should judge the work on the intrinsic merits of the work, not the worker. Every human has the right to work and be evaluated on the work, independent of the nature of their birth.