In general coordinates the basis changes along the world line. Differentiating only the components of a vector omits that basis change, and does not transform as a vector under a position-dependent coordinate transformation. The appropriate rate is the covariant derivative along a curve:
For the metric-compatible torsion-free connection, the Christoffel symbols are determined by the metric tensor and its first derivatives:
Thus the ship's four-acceleration is
In Cartesian coordinates of an inertial frame in flat spacetime, the connection coefficients vanish and the ordinary component derivative happens to suffice. In curved spacetime it suffices at a chosen event in a local inertial frame, but not generally along an extended trajectory.

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