correctness of the perldoc asside, there are two very differnet use cases here. In the first case, you want to disable the code and keep it from ever running, but it will still be parsed and validated for syntactic (and semantic) correctness. This can be very advantagous when you want to temporarily disable some code, but you don't want anyone to move, remove, or refactor variables or functions that it calls. In the second case, by making the lines perldoc, their content is irrelevant, and you're free to do whatever you want.
Frankly, if you are using a decent text editor or IDE, it should be trivial to comment out a large number of lines with a simple macro, and it should be jsut as simple to uncomment then later. And i find it a lot easier to spot at a glance when a large chunk of code is commented out then to tell when a large chunk of code is "poded out". Even when I'm working with java, which supports both a prefix comment marker, and a delimiting comment marker, i always use the prefix comments to comment out a large chunk of code. that long column of comment characters really jumps out at you.