In case of 550D the central AF point is both horizontal and vertical and is better than the peripheral points. Shouldn't be a problem It doesn't matter if you are using back button focusing or using shutter button half pressed.

Handholding at 400mm will result in some drop in sharpness depending on technique and shutter speed. It shouldn't be an issue regarding the focus point.

To check the lens front focusing, just tape a newspaper on your wall and then click. You can then see if the focus point is fine or not.

However, the reason why the critical focus is on the leaves and not on birds is that your camera locks focus based on higher contrast. The AF is based on contrast detection.

If you had set an aperture of f11 or so, then the bird would have been more in focus due to higher depth of field. Thanks for sharing.

Cheers,
Sabyasachi