Just a general piece of advice, but it's best to avoid hand-rolling your own CSV parser. Use Text::CSV instead, preferably with Text::CSV_XS also installed so you get the speed boost.

As for handling arguments, you can use Boolean assignment in many cases. For example this

$columnSeperatorChar = "," if ($columnSeperatorChar eq "");
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can be written as

$columnSeperatorChar ||= ",";
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(assuming you will never use a 0 as a column separator)