Unless you have reason to split the first n-1 pieces as well, you only need the last one separated.
Once you have it, you replace the commata with quote, newline, appropriate number of spaces, quote
Voila!
while(<DATA>) {
chomp;
my ($first, $last ) = /(.+",)(.+)/;
print $first;
$first = " " x length( $first );
$last =~ s/,/"\n$first"/g;
print "$last\n";
}
__DATA__
"A","B","C","D"
"A","B","C","D,E,F"
"A","B","C","D"
"A","B","C","D,R,T"
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