Why? Do you mean the perl scripts 'source' encoding? That doesn't really matter here.
Perl's impression of what \r and \n mean differs from system to system. A Mac would output \015 when it sees \n while a unix box would generate \012 (IIRC now, it might also be the other way round... ;).
So if a script tries to handle DOS text files using \r\n to split, chomp, substitute, etc. input, it will work on a system that has a compatible native encoding (ASCII). If, however, you run the same script on a noncompatible system (for example on an EBCDIC platform like IBM's AS400, or even something more common like a Pre-OS X Mac) it will do really funny things with your input, as it translates \r\n to some other ordinals, regardless of the scripts source encoding (which will most likely be the platforms "native" encoding).
Same is true of course, when you want to operate on files coming from AS400 machines on your unix box (which is more likely, I guess). If you'd try split these files on (unix') \n, you'll hit anything but a line end...
To sum up: DOS files want to be split on \015\012, regardless of what line terminators the splitting sytem uses...