The truth about these numbers is much more mundane. Simply put, the way the abilities are coded, all of the green numbers are variables.
Runes used to have quality levels, with each successive level of rune increasing the efficacy of the skill. This is why runes like Arcane Torrent's Cascade list "a 100% chance", instead of saying "whenever" or "always" -- if you used a lower level rune, it wouldn't be a 100% chance.
For Abilities and Passives
For abilities, the thinking is mostly the same, though the rationale is different. Essentially, by designing the abilities in the way that they did, they've made it very easy to tweak and balance the individual abilities against each other.
Consider, if you will, Bolas Shot.
Notice which values are in green: The hatred generaiton, the delay, the initial damage, the splash damage, and the splash range. Now imagine that Blizzard determines bolas shot to be horribly, horribly overpowered. They have to nerf it. What do they change? Well, because of the way they built the game, they already have 5 "knobs" to tweak in an attempt to better balance it - the five variables in green. Even when one of the green values isn't affected by any of the five runes, it's still useful as a tuning mechanism.
This happened in beta all the time - the balancing patch notes would always tweak the green values, and leave the rest of the ability untouched.
There is also a subclass of skills and abilities which have the green text because they scale with level.
Most healing abilities are this way. In these cases, the text is green to signify that the value is not constant (because, again, everything in green is a variable), and is used instead of listing a formula (which would be constant, but would be bothersome to calculate manually each time it changed).
Even here, the underlying formula can be changed, with the same results as tweaking the formula in one of the non-scaling abilities above.