As I understand it, the writer is trying to convey the opposite of what you suggest.
The fact that Vega muttered, "Just as long as we understand each other" means he was saying that they both knew they were enemies and would still kill each other if they got the chance even though neither of them really knew why.
A field base is a kind of mini army camp in a combat zone -somewhere soldiers return to in order to get back together. They must have agreed on a meeting place so that became a kind of makeshift field base.
Hope this helps