It is a nuclear wasteland, it's perfectly reasonable he would be prepared for radiation. And the troopers, they're probably expendable.
Yes, it's reasonable to be prepared for radiation, and for normal wasteland travel, good ol' Rad-X and Rad Away suffice. You do expect to come across radioactive waste, mutants, water, and so on and so forth. Obviously though, the irradiated chamber was a special, particularly lethal case, and normal Rad-X and Rad Away weren't sufficient to survive bombardment. That meant a specially prepared medicine was needed, and how the heck did Autumn just happen to be carrying this perfect defense on his person?
Basically, it still seems contrived and implausible to me. If it didn't, would we even be having this discussion? No one would have noticed this as a potential plot hole at all if the scenes had been handled better to begin with.
I checked the wikia, and found this; Contrary to a comment about Fawkes' gender made by his voice actor, lead designer Emil Pagliarulo has confirmed "No, Fawkes was absolutely a male. This was a mistake. Wes gave an interview and he was mistaken. Trust me, Fawkes is and was male." http://fallout.wikia.com/wiki/Fawkes
I agree, it's a bit of a cheap way out, but I wouldn't say it's breaking the fourth wall, more of a deus ex machina.
Well, I can't blame Fallout 3 for the gender blunder. In Fallout 2, if you pay for a hoker for Marcus, he tells the Chosen One that Super Mutants aren't actually sterile. The developers later stated that Marcus was wrong, and that they are in fact sterile.
As for Fawkes' refusal to enter the chamber being a
deus ex machina (which means "god from machine" [I knew that years ago, I didn't Google it
]), not quite. That's actually the opposite of what we're talking about, which is a refusal to help. Here's the Wikipedia definition of the term:
"A deus ex machina (pronounced /ˈdeɪ.əs ɛks ˈmɑːkinə/ or /ˈdiː.əs ɛks ˈm?kɨnə/,[1] literally "god from the machine") is a plot device in which a person or thing appears "out of the blue" to help a character to overcome a seemingly insolvable difficulty."I'm not sure what you'd call the plot device that is Fawkes' refusal to help for no other reason than to support the plot. The best I can come up with is "cop-out."