I've edited my post above to make clear that the angle in my equations is the angle that the rod makes with the x-axis, in the rod's rest frame. That is, it's the "original" angle.
In a frame in which the rod is moving, the angle is different, except if the angle is either 0 or 90 degrees to begin with. That is, if the rod is parallel to the relative velocity, in its own rest frame, it is parallel in the other frame. Likewise if the rod is perpendicular to the relative velocity.
To see this, start with the angle of the rod in the "moving" frame:
\cos \theta = \frac{L_x}{L}
Using the other equations in my previous post, you can find
\cos \theta =\frac {\cos \theta_0 \sqrt {1 - \frac {v^2}{c^2}}} {\sqrt {1 - \frac {v^2}{c^2} \cos^2 \theta_0}}
See what happens when \theta_0 = 0 and when \theta_0 = 90^\circ?