From looking at the pics and from personal experiences :
Image 1 shows light zones. These are used on the mapping software to dictate how intense light is and to which direction the sun is facing. Seeing that seems to be a client issue. For the other 2 i have no idea.
Another thing to note: there is currently no way to sent crew members on missions ect while being physically offline. This will more than likely change in the future.
N(default) access crew skills.
For crafting you can queue 5 at a time that when made go into your inventory. If you have no space then it goes to "pending missions" (top right)
These items will be made regardless if your on or not aslong as you set them going.
Same applys to gathering, just set them off and it doesnt matter if your on or not.
You can assign your crew members to do any thing you want them to.
For gathering, money is deducted as soon as you send them. If you cancel it your money gets refunded.
Note : you can only queue 1 gathering at a time per crew member.
Basically says it all.
Armor / hilt change the base level of the item as well as the armor rating / minmax hit.
Other mods change base attributes such as will power, strengh, power ect.
Pvp sets only directly impact preformance in pvp situations e.g. "3/4 = +5% damage of X to players"
Orange gear is good (personal fav) due to the fact they can be constantly updated (at a price) to be what the user desires.
There are pve sets which do the same as pvp sets.
Its all down to user prefrence.