I'm fairly sure that "the code is the spec" applies to arc.arc, not to ac.scm. That is, anything that can interpret arc.arc properly is a conforming Arc implementation; ac.scm is just one of them. And since nil is (), then in Arc, your two lists are the same but with different formatting. Observe:
arc> (is nil '())
arc> (is nil ())
arc> (iso '(a b c) '(a . (b . (c . nil))))
arc> (iso '(a b c) '(a . (b . (c . ()))))
arc> (iso '(a . (b . (c . nil))) '(a . (b . (c . ()))))
So even if you put #f in the terminating position, your lists will still be iso.
arc> (iso '(a b c) '(a b c . #f))
Are you saying that arc lists are #f terminated just because it doesn't break arc to put #f in random lists? Even if arc lists can be terminated by nil, (), and #f, it doesn't mean they necessarily are. Any given list (ignoring nested lists) can only have one termination object. I think it is reasonable to say that that list is terminated by that object. I do not think it is reasonable to say that list is terminated by another object, even if it could be, because the actual object at the end of the list is not that other object. And because the current implementation (the only official implementation) uses nil, I think it reasonable to say that arc lists are terminated by nil. Note the use of the present tense. If that changes at some future time, I my statement will obviously not apply.
In short, given the current implementation, we have (at least) six different ways to write nil: nil, 'nil, (), '(), #f, and '#f. These six things are all considered identical within Arc. The same is true, for instance, of 'a and (quote a), which are the same thing entered differently. You can check that they are the same with is; I won't put all those examples into this post.
I have never said that Arc lists aren't nil terminated--clearly, they are. What I'm saying is that Arc lists are nil terminated for any representation of nil--whether that representation is nil from Common Lisp, '() from Scheme, or #f from a leftover artifact of using the mzscheme reader.