I suspect there is no "good and fast" solution. This problem, to me, has the flavor of a permutation or "traveling salesman" problem, and is probably NP-hard (or one of the other NP classes).

So here's an attempt (with a cheat) that at least gets a solution in a sort of reasonable time for this problem.

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11118281
use warnings;

my @list=("set abcde-efghi 12345",
          "set abcde-ijkl 12345",
          "clr abcde-efghi+123",
          "clr abcde-ijkl 12345");

#my @expected_substrings=("set","clr"," abcde-","efghi",
#                         "ijkl"," 12345","+123");
#my $len=@expected_substrings*2;
#$len+=length($_) foreach @expected_substrings;

$_ = join "\n", @list;
my $max = 3; ########################################### BIG CHEAT FOR
+ RUNTIME

sub score { 2 * @_ + length join '', @_; }
my $best = score( @list );

try( $_ );
print "\n";

sub try
  {
  (local $_, my @sofar) = @_;
  if( !/[ -~]/ )
    {
    my $score = score @sofar;
    if( $score < $best )
      {
      print "\n";
      use Data::Dump 'dd'; dd $score, @sofar;
      $best = $score;
      }
    return;
    }
  score(@sofar) >= $best and return;
  for my $n ( reverse 0 .. $#list )
    {
    my %d;
    /([ -~]{3,})(?:.*?\1){$n}(?{ $d{$1}++ })(*FAIL)/s;
    my @d = sort { length $b <=> length $a } sort keys %d;
    @d > $max and $#d = $max - 1;
    for my $string ( @d )
      {
      try( s/\Q$string\E/\t/gr, @sofar, $string );
      }
    }
  }
[download]

Outputs:

(46, " abcde-", " 12345", "efghi", "ijkl", "clr", "set", "+123")
[download]

where the "46" is the score and the rest are the substrings. As it finds better scores, it will print them, but so far always seems to find a best solution first.