I am having some trouble reconciling the Minkowski (4-dimensional) and the pre-Minkowski (3+1-dimensional) approach to special relativity. Let me describe (how I interpret) the Lorentz transformations in these two approaches.
3+1 view
There exist two reference frames, $S(t,x,y,z)$ and $S'(t',x',y',z')$ so that $S'$ moves with velocity $\vec{u} = u \vec{e}_x$ with respect to the frame $S$. We can take the axes of the two frames to be parallel $\vec{e}_x = \vec{e}_{x'}$, $\vec{e}_y = \vec{e}_{y'}$ and $\vec{e}_z = \vec{e}_{z'}$. Here, it is assumed that the basis vectors of both frames live in the same vector space so that we can compare and equate them.
Now, let us relate the description of motion in these two frames. If a particle moves with velocity $\vec{v} = v^x \vec{e}_x + v^y \vec{e}_y + v^z \vec{e}_z$ in $S$ and with the corresponding velocity $\vec{v}' = v^{x'} \vec{e}_{x'} + v^{y'} \vec{e}_{y'} + v^{z'} \vec{e}_{z'}$ in $S'$, then the Lorentz transformations imply the following transformation law for the components of the velocities $$v^{x'} = \frac{v^x - u}{1 - \frac{u v^x}{c^2}}, \quad v^{y'} = \frac{1}{\gamma}\frac{v^y}{1 - \frac{u v^x}{c^2}}, \quad \quad v^{z'} = \frac{1}{\gamma}\frac{v^z}{1 - \frac{u v^x}{c^2}},$$ where $\gamma = (1-u^2/c^2)^{-1/2}$ is the standard Lorentz factor. Now, we can multiply these transformation laws with the appropriate basis vectors and sum to obtain the transformation law for the velocity vector (and not just the components) $$\vec{v}'_\parallel = \frac{\vec{v}_\parallel - \vec{u}}{1 - \frac{\vec{u} \cdot \vec{v}}{c^2}}, \quad \vec{v}'_\perp = \frac{1}{\gamma} \frac{\vec{v}_\perp}{1 - \frac{\vec{u} \cdot \vec{v}}{c^2}}.$$ Here, parallel and perpendicular is meant with respect to $\vec{u}$. The two last equations make perfect sense since all involved vectors are elements of the same vector space.
Minkowski view
In Minkowskian view, the two reference frames are described by two tetrads $\{\vec{e}_t, \vec{e}_x, \vec{e}_y,\vec{e}_z\}$ and $\{\vec{e}_{t'}, \vec{e}_{x'}, \vec{e}_{y'},\vec{e}_{z'}\}$ which are related via hyperbolic rotation $$\vec{e}_{t'} = \vec{e}_{t} \cosh \chi + \vec{e}_{x} \sinh \chi, \quad \vec{e}_{x'} = \vec{e}_{x} \cosh \chi + \vec{e}_{t} \sinh \chi,$$ so that, while $\vec{e}_y = \vec{e}_{y'}$ and $\vec{e}_z = \vec{e}_{z'}$, the $x$ and $x'$ basis vectors do no longer coincide $\vec{e}_x \neq \vec{e}_{x'}$.
So, the first puzzling differences between the two approaches is that they do not agree on the equality of the basis vectors.
Let's see what this implies for the velocity transformation. A particle with four-velocity $\vec{V}$ is equally well described in both frames, $$\vec{V} = V^t \vec{e}_t + V^x \vec{e}_x + V^y \vec{e}_y + V^z \vec{e}_z = V^{t'} \vec{e}_{t'} + V^{x'} \vec{e}_{x'} + V^{y'} \vec{e}_{y'} + V^{z'} \vec{e}_{z'},$$ where the transformation laws for the components is inherited from the transformation law for the basis vectors $$V^{t'} = V^{t} \cosh \chi - V^{x} \sinh \chi, \quad V^{x'} = V^{x} \cosh \chi - V^{t} \sinh \chi,$$ and $V^{y'} = V^y, V^{z'} = V^z$. The standard relation between the three- and four-velocity is taken to be $$\vec{V} = V^t (\vec{e}_t + \vec{v}/c) = V^{t'} (\vec{e}_{t'} + \vec{v}'/c).$$ If we write the 3-velocities in terms of the components, we have $v^k =c V^k/V^t$, with $k \in \{x,y,z\}$ and similarly for the primed vector. From the known transformation laws of the components of the 4-velocity, we can deduce the transformation law for the components of the 3-velocity $$v^{x'} = \frac{v^x - c \tanh \chi}{1 - \frac{v^x c \tanh \chi}{c^2}}, \quad v^{y'} = \frac{1}{\cosh \chi}\frac{v^y}{1 - \frac{v^x c \tanh \chi}{c^2}}, \quad v^{z'} = \frac{1}{\cosh \chi}\frac{v^z}{1 - \frac{v^x c \tanh \chi}{c^2}},$$ which agrees with the 3+1 transformation law for the components of 3-velocity if we identify $u = c \tanh \chi$ and $\gamma = \cosh \chi$. However, in contrast to the 3+1 approach, we can no turn the above transformations to vector transformations because $x$ and $x'$ basis vectors no longer point in the same direction.
My question: What is the correct way to interpret this "paradox"? Also, what is the correct interpretation of the velocity-addition formula? Does is hold only component-wise, or at the level of 3-vectors?