In a differential geometric setting, the covariant derivative can be defined as a map $\nabla_X:\Gamma(TM)\to\Gamma(TM)$, for any vector field $X\in\Gamma(TM)$, satisfying certain conditions. In other words, for any vector field, it maps vector fields into other vector fields. This definition is then readily extended to maps between arbitrary tensor fields. Given a local basis $\{\partial_i\}_i$ around some $p\in M$, it can be characterised via the Christoffel symbols as $$\nabla_i\partial_j\equiv \nabla_{\partial_i}\partial_j =\Gamma^k_{~~ij}\partial_k.\tag1$$ Similarly, we get local expressions such as $$\nabla_i Y = \nabla_i (Y^j \partial_j) = (\partial_i Y^j + Y^\ell Y^k \Gamma^j_{~\ell k})\partial_j.\tag2$$
So far, so good. My confusion arises when trying to match this with the notation used in more physical contexts. For example, consider these lecture notes ([29:46] on youtube). Here, they denote the covariant basis as $\vec S_\alpha$, and write the Christoffel symbol as $$\Gamma^\gamma_{~\alpha\beta}=\vec S^\gamma\cdot\partial_\beta \vec S_\alpha.\tag3$$ When writing this, they're assuming to be dealing with embedded surfaces, so taking the standard derivative still makes sense, and I can match this expression with (1) assuming the covariant derivative to be the projection of the standard derivative on the tangent surface.
However, from (3) they derive $$\vec S^\gamma\cdot(\nabla_\alpha\vec S_\beta) = \vec S^\gamma\cdot ( \partial_\alpha\vec S_\beta - \Gamma^\omega_{~\alpha\beta}\vec S_\omega ) = 0.\tag4$$ This appears now to be in direct contrast with (1), as $\vec S_\alpha$ in (4) should correspond to the local basis for the tangent space, $\partial_i$, in (1). In fact, following this notation, $\nabla_\alpha \vec S_\beta$ is normal to the surface, which seems in direct contrast with the definition of covariant derivative in (1), an an object mapping tangent vectors into tangent vectors. So what gives? Why are these two notations seemingly in contrast? Is there a more formal way to understand precisely what kind of object the covariant derivative is in the latter convention?