Why does A2 say “Command is the one that betrayed you”

Ah, the big choice.

Since the ending sequence is nigh impossible without accepting help (this is clearly intentional, as the entire point is that you can't take on enormous tasks alone), you accepted it, right? Every person that assisted you was actually someone who chose to erase all of their save data for this purpose. Had you chose to delete your save, someone out there who needed help on the ending sequence would have gotten assistance from you.

I originally declined in order to 100% the game, but as soon as I had done so, I went back and redid this sequence so that I, too,

could erase all save data in order to assist someone else.

If you choose yes, you will actually be prompted for confirmation about 7 or 8 times before it actually happens.

During the sequence directly following, it will show all of your data being deleted, one item at a time (though many are skipped over so this doesn't take an eternity). The very last part shows all of your save slots being erased. This means you cannot simply copy your save data to a second save data slot. All three are erased entirely. The only record of you having played the game and made this choice is that you will get an alternate background for the title screen. It looks like this:

As someone who also repeatedly died on the first level and had to replay it many times, I vividly remember this dialogue. A lot of the "significant" things won't really stand out until you've reached the true ending, so although I'm going to explain within spoiler tags, don't take them lightly.

1. Yes.

2. I honestly don't know exactly what is said, but from the bits I was able to pick up, it sounds like a mix of some prerecorded announcements and messages for the factory while it was still in use by humans before they left.

3. See spoilers below, but as I said before, this includes very important plot points, so proceed with caution...

The fact that 9S says that nothing machines say make any sense is a bit ironic after you discover that YoRHa androids' black boxes are repurposed machine lifeforms cores. That is to say, YoRHa androids are essentially just prettier machine lifeforms. The YoRHa androids only differ from machine lifeforms in that they were created by different things. The argument that they look different is disproven when the machine lifeforms create Adam and Eve. This line in particular isn't exactly significant story-wise (however, the idea that androids are superior or otherwise different from machine lifeforms is a recurring theme and you will see dialogue like this throughout the game), it is something that you will pick up on when you hear it again after completing the true ending and learning the truth about everything.

Another reason this is important is that is a subtle hint towards the fact that is revealed much later on that machine lifeforms were created with the purpose of "destroying their enemy," however, they eventually realized that without an enemy, their existence is meaningless. Thus, they will never fully destroy the androids. In an effort to ensure this, they allowed themselves to be created with imperfections and anomalies that would hinder their own attack power. Examples of these anomalies would be Pascal, the Forest King, and the machine lifeforms who express more human traits, such as speech.

As for what the Goliath machine lifeform said outside the facility, unless I missed something, I'm pretty sure that one only repeats "KILL... KILL... KILL..."

However, you will meet MUCH more articulate machine lifeforms later on.