Hi!
Strictly speaking, a skimmer on first fire orders engaged in close combat by a skimmer is NOT pinned. Heck it doesn't even need to fire at the non-skimmer unit that charged it!
Of course it means it can be picked off from afar by a unit external to the "close combat". Of course the skimmer could opt to voluntarily be pinned by the non-skimmer unit.
A rule set is mainly a guideline. When we added the rules, they were mainly "plugged" into the original frame without changing that frame. This means its easier to choose some rules not others. In essence you can cherry pick which rules to use on top of the original framework and still have a viable play experience.
So no worries on liking some and not other rules. Its expected and encouraged. Heck if you have made up some other stuff we'd like to hear about it!
On another note, the extra additions were made with a "combined arms" approach. If your using all the rules and not using aircraft and AA fire units, then depending on which army you play you may have a harder or easier time.
So I would not include several of the rules if you don't use fliers.
A lot has been said regarding fliers and their rules throughout the years. We've gone from more detailed flier rules to less, from optional to alternate rules. This underscores the point that air power IS significant, so if one side uses them and the other does not it may be a lopsided battle.
However its simple to leave them out altogether. A lot of people like to play epic as a ground battle with no fliers at all!
In the end there is no "right" or "wrong" way to play, only the "fun" way which is "your" way.

Primarch
Primarch