You are asking a series of questions that are complicated. First off, they recommend that you transfer 6.5 gallons instead of the 6.64 that you should have ended up with in your boiling kettle according to their estimation because they expect you to leave some wort behind because it will be thick with hop material. You don't need to leave this as it will have wort that can make beer in it and the hops will settle out at the end of the fermentation. When fermentation ends and you allow the resulting beer to have time to clear there will be a bunch of proteins and hops in the bottom of the fermenter that you will leave there when you transfer to your bottling bucket, about half a gallon. That's why you transfer 6.5 when you expect 6 gallons to bottle.
When you use a recipe for all grain, the recipe is designed for a particular brewhouse efficiency. Yours was lower than that which got you a lower OG. Two reasons for that. One is the quality of the milling of the grain which is what drives the efficiency. Second is the amount of wort you actually got and transferred. The recipe expects you to boil off about 1 1/2 gallons of water. I think that is way too much as it takes a strong boil for a long time to boil off that much. I typically only boil off 1/2 gallon. Now with this much experience, you can start adjusting recipes to account for how you brew instead of how someone else brews.