|more useful options|
I understand your reasoning, and for most languages you would be correct. But Perl is different: in Perl, the behaviour of functions and operators depends on context. For example, here is what the documentation says about backticks:
The collected standard output of the command is returned ... In scalar context, it comes back as a single (potentially multi-line) string, or undef if the command failed. In list context, returns a list of lines ..., or an empty list if the command failed.
So, in your script:
the expression `cat file.pl` is in scalar context (because split expects a scalar expression here), so the output of the cat command is fed to split as a single, multi-line string. But in your other script:
the assignment to an array (@lines) puts `cat file.pl` into list context, so the output of the cat command is here not a single string as before, but rather a list of strings (one for each line).
Context is a central concept in Perl. You can read up on it in the references given by Anonymous Monk, above, or in Chapter 2 of Programming Perl by Christiansen, foy, and Wall (in the section beginning on page 76 of the 4th Edition).
Hope that helps,
Athanasius <°(((>< contra mundum