The secondary can be too far up the tube, too far down the tube, and slightly uncentered under the focuser, not to mention slightly off-round, and still be collimated. There are many optical configurations where these other positions are PURPOSELY chosen.
The centering of the secondary under the focuser (essentially offsetting the secondary toward the primary, but not away from the focuser) is to result in even edge illumination for the light cone from the primary.
If you draw a cross-section of a reflector on graph paper, you will see that the primary mirror's beam does not strike the exact center of the centered secondary mirror--it strikes a little lower than center (toward the primary) on the secondary mirror. This is because the light cone gets narrower the farther it is from the primary, and it is narrower when it strikes the part of the secondary farther from the primary.
That means the edge of the secondary farthest from the primary fields none of the axial light beam from the primary, and more of the off-axis light than the part of the secondary closest to the primary. So we drop the secondary closer to the primary to evenly illuminate the edge of the secondary (which is what happens when you center the secondary in the focuser). The center of the beam from the primary now strikes the secondary slightly away from the exact center of the secondary (offset, essentially, up the secondary away from the primary), but we achieve better edge-of-field illumination.
If the secondary is slightly off-center, does it matter? No. It just means (and it probably won't be visible) that the edge-of-field illumination won't be exactly the same all the way around.
Can the secondary be rotated slightly around its axis and still be collimated? No. The return reflection of the primary mirror's center mark will not line up with the crosshairs in the sight tube. So the sight tube will correct the misalignment even if the mirror is slightly out of perfect position.
If you're really fussy and want to have everything perfect, a telescoping sight tube, a good cheshire, and a good autocollimator will allow collimation to the small thousandths of an inch.
I recommend Catseye tools. There are also some excellent tutorials on collimation on Jim Fly's site. see:
www.catseyecollimation.com
Don