The percentage line height is a percentage of the default line height specified by the font designer. For many fonts, the default line height is 120% of the font size, but this can vary quite a bit (e.g. for Zapfino it is 340%). The actual line height is calculated using the formula font size × line height × default line height.
For example, if the font size is 10px, the line height is 100%, and the default line height is 120%, the actual line height will be 12px (10 × 1.0 × 1.2). If we increase the line height to 120%, it will be 14.4px (10 × 1.2 × 1.2).
If you want explicit control over the line height without considering the default line height multiplier, you can enter pixel values. For example, if you explicitly want a 13px line height, simply enter 13px into the line height field.