Unfortunately most of what you learned is just not true. What likely happened when you ran the cartridge completely out of ink is that air was ingested into the printhead. When you take out a cartridge and put the same cartridge back in (whether refilled or not) it will not go through the extra initialization that a new cartridge would get. When you removed the printhead you triggered a full initialization once the printhead and cartridges were replaced. The extra initialization removed the air, allowing the ink to prime the printhead.
The alignment will fail if either black or the color used for alignment (typically cyan or yellow) fail to properly print.