Does "you were both of aware" and "both of you were aware" mean the same here?

How different "come from up" and "come up from"?

To "come from up" means that something came from somewhere that is above or in an upwards direction. To "come up from" includes the phrasal verb "come up", which means that something arose or appeared from somewhere, but it does not always have to be in an upwards direction. Ex: This box came from up in the attic. Ex: He came up from Florida to visit.

Why did she say "lights out" not "lights off"?

In general, native English speakers say "lights out" when turning off lights, especially before bed. It's common to tell children "turn the lights out" or "lights out at 9pm" to tell them to go to bed. Lights out/lights off have the same meaning, but like I said it is common to say "lights out".

Is the sentence complete without "it is" at the end?

Good question! When we see "it is" at the end of a sentence, we can understand it as a confirmation of the statement preceding it ("earth as the giant interconnected system). You can see it in situations when one wants to confirm the correctness of a choice for something. Ex: A: Do you wanna meet on Friday? B: Sure! Friday it is. Ex: A: What flavor of ice cream do you want? B: Cherry please! A: Cherry it is.

Does "you were both of aware" and "both of you were aware" mean the same here?

"You were both of aware" is not correct. "Both of you were aware" and "You were both aware" have the same meaning.

What's "whilst?" Is is same as "while?"

As a conjunction and an adverb, they mean the same thing! They mean during or at the same time as something, or they indicate a contrast. However, you can't use "whilst" as a noun the same way we use "while" to mean a period of time. "Whilst" also sounds slightly more formal and is probably considered more British English than American. Ex: I'll read a book while you play soccer. = I'll read a book whilst you play soccer. Ex: While the walls were a nice blue, the door was a horrendous red. = Whilst the walls were a nice blue, the door was a horrendous red. Ex: It took a while for them to get here. => correct = It took a whilst for them to get here. => incorrect