This point was raised two years ago when I first distributed the module via CPAN. My feeling then was that the fact that the lists being compared were real-world data sets (I can hear my boss saying, "Get me a list of ...") was more relevant to its naming than the fact that the lists were placed into arrays before being passed to the constructor.
I think the point is less valid today, because now the lists do not necessarily be in the form of arrays before being passed to the constructor (or passed to function in List::Compare::Functional). Now, you can pass seen-hashes to the constructor or function -- seen-hashes which imply the existence of underlying lists. See the documentation on seen-hashes
Dave, I looked at Array::Compare when preparing the documentation. It seems to me that your approach is more tightly focused on comparing Perl arrays and takes a different approach to determining 'sameness' than does List::Compare. The two modules are tackling different problems.