I found out what is going on, PDL does double-buffer, at the line:

# PDL/Graphics/TriD/GL.pm" line 789
sub display {
    # ...
    $this->{_GLObject}->glXSwapBuffers();
}
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display is called from twiddle which does the model fly-through stuff. My flicker came from using hold3d, points3d then imag3d_ns but points3d calls graph_object (calling twiddle_current then twiddle), so the points were drawn, the buffers swapped making imag3d_ns seem to flicker. I just need to avoid the points3d shortcut, and other forms using graph_object.

Brad