This episode always bothered me. Actually, I think it is the worst Voyager episode. Ruined Scorpion 1+2 for me. Now that I think of it, I'd rather watch Threshold than "In the Flesh". The Ultimate Xenophobic race, best friends of mankind in 40 minutes, thanks to Chakotay. Oh, dear.
Also, it's full of plot holes. WHY is the staging area there in the first place, THOUSANDS of lightyears from Earth? There are supposedly more of these domes, but this Boothby character happens to be the big leader who can stop every Sp8472? Quite a coincidence.
"These are the Voyages..." is a masterpiece compared to this drivel.
I think you need to rewatch the episode again, you're missing details that explain your questions. The "staging" area is there because 8472 thinks that humans are dangerous, they are learning to act like them so they can get some spies into the Federation and observe them to see if they are truly a threat or not
Bothby was far from the "big leader who can stop every 8472" watch the episode, he was kind of the leader of that particular group, he said that he would go to the other groups and propose the peace agreement to them, but he was doubtful they would agree to it.