I suggest the below code as the consolidated answer to my question, if there are no objections. The handling of blanks is redundant but could be modified for other purposes.

#!/usr/bin/perl -w

my @AoA = (); # ArrayOfArrays

# read data plus add index
while (<DATA>){
  s/\s*//g;
  my @tmp = split ',',$_;
  $tmp[0] *= 1.0;
  $tmp[1] /= 1.0;
  $tmp[2]  = $.;
  push @AoA,\@tmp;
}
# or
#push @AoA, [split(/,\s*/, $_)] for <DATA>;
#push @{ $AoA[$_] }, $_ for 0 .. $#AoA;

# modify columns
foreach my $row (@AoA) {
    foreach my $item (@$row) {
        $item =~ s/^\s+//;
    }
    $row->[0] *= 1.0;
    $row->[1] /= 1.0;
}
# or
#($_->[0] *= 1.0, $_->[1] /= 1.0) for @AoA;

# screen output    
printf "%e,%e,%d\n",@$_ for @AoA;

__DATA__
0.00000000e+00, 2.41644835e+00
1.20048018e-04, 2.38938189e+00
2.40096037e-04, 2.36473989e+00
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