Way back in the early days of Perl 5 substr didn't have the facility to supply a fourth argument so assigning to it as you describe was the only way to go. The advantage of using the 4-arg form to replace text is that what has been replaced is returned. Thus you can chain substrs together to move text around.

knoppix@Microknoppix:~$ perl -E '
> $str = q{abcdefghijk};
> say $str;
> substr $str, 5, 2, substr $str, 3, 2, substr $str, 5, 2;
> say $str;'
abcdefghijk
abcfgdehijk
knoppix@Microknoppix:~$ perl -E '
[download]

Of course, that particular example can be done more simply with a regex substitution but it can be a useful technique sometimes.

knoppix@Microknoppix:~$ perl -E '
> $str = q{abcdefghijk};
> say $str;
> $str =~ s{^...\K(..)(..)}{$2$1};
> say $str;'
abcdefghijk
abcfgdehijk
knoppix@Microknoppix:~$
[download]

I hope this is of interest.