Ok, so to just look at what happens in the scenario that Bob describes. In the train's rest frame in Bob's scenario, we have the following situation:
Here, the crate is traveling straight at the window with at speed ##v## and with the sides parallel to the train. The world lines of the points 1-3 can be described by
$$
x_1 = vt_1, \quad y_1 = 0, \quad x_2 = vt_2 + \frac \ell{\gamma_v}, \quad y_2 = 0, \quad x_3 = vt_3, \quad y_3 = \ell.
$$
Lorentz transforming to the ground frame, traveling at speed ##u## relative to the train, and evaluating at the same time ##t' = 0## results in
$$
(x_1', y_1') = (0,0), \quad (x_2',y_2') = (\ell/\gamma_v,0), \quad (x_3', y_3') = (-uv\ell, \ell/\gamma_u).
$$
We therefore have the following situation in the ground frame:
It is clear that this is not the same situation that is obtained from just boosting the crate from an orientation parallel to the train as described by Alice. Instead, it is something that is obtained by boosting a rotated crate. In the situation described in the OP, where the boost is at velocity ##1/\sqrt{2}## at an angle of ##\pi/4##, we can find the required rotation angle geometrically:
Here, the red lines are the directions parallel/orthogonal to the boost. The contraction occurs along the line tilted to the NE/SW and we require the top black line to contract into the green line. This means that the contraction along the boost direction must be given by ##\gamma = \tan(\pi/4 + \theta)## where ##\theta## is the rotation angle before the boost. Solving for ##\theta## gives ##\theta = \tan^{-1}(\gamma) - \pi/4##. In particular, if ##v = 1/\sqrt{2}## then ##\gamma = 1/\sqrt{1-1/2} = \sqrt{2}## and so ##\theta = \tan^{-1}(\sqrt 2) - \pi/4##. This corresponds to a rotation of ##\theta \simeq 10^\circ##.