Soo many misconceptions here.
First off, sorry for the delay in a detailed reply - I was out of the country for the past week.
1. There is ZERO need for any clarifications in the docs. If you're looking to create an ability that acts like/follows the rules of an existing ability in the system, then you use that. If you don't want the special rules of an ability like, say, Computer Programming, then don't use it -- stick with the general Skill definition/rules.
2. Know the rules of the ability you're trying to mimic before trying to create a custom template. To use Computer Programming as an example, it defaults to a 3/2 Skill (3 points for the Skill itself, 2 points per level increase). If an Adder is chosen, then it changes to 2 points (plus any additional Adders/categories) for the Skill itself and 2 points per level increase. Note that even under the 5th Edition Rules, if you only select a single sub-category it's going to cost you 2 points....again, know the rules of the system. Select a category and a (separate) sub-category and you'll see that 1 point per sub-category come into play. Even under 6E.
3. I REALLY don't recommend modifying either of the Main templates -- extend the appropriate one. In particular, you'll want to extend one of the genre-specific templates (e.g. SuperHeroic6E.hdt) in order to take full advantage of many of the rules switches in HD's code -- there are numerous checks/switches for 5th Edition vs. 6th Edition, Heroic vs Superheroic, etc.
4. If what you're after is a fine-grained, real-world adaptation of computer programming abilities, unclevlad is pretty much spot-on: 5E is in no way, shape, or form a more realistic way to model it -- that's why it was dropped in 6E. If you really wanted to do something different, look to leverage Languages for Computer Programming...though putting together that particular familiarity chart is not a task for the faint of heart.