Elegance and wit are in the mind of the beholder - my favorite solutions are the ones that work and work reliably. In any case, since you have synchronized arrays, you have a couple of options for how to traverse them - e.g. you can either use an index variable as you have done or you can use shift to destructively-traverse one or more of the arrays, as I have done below. As well, rather than the branching you have done, I took advantage of the fact that printf silently drops unused terms to move the conditional into the format statement. I have also abstracted the field-size and precision to variables at the top of the script to aid in future-proofing.

#!/usr/bin/perl
use strict;
use warnings;

my $best = {1 =>[1,2]};
my $kept_best = {1 =>[1]};

my $width = 10;
my $precision = 5;

printf "%-${width}s %-${width}s\n", "BEST", "SELECTED BEST";
foreach my $value (sort keys %$best){
    foreach my $bind_energy (@{$best->{$value}}){
        my $kept = shift @{$kept_best->{$value}};
        
        my $format = "\%${width}.${precision}f";
        $format .= defined $kept ? " $format\n" : "\n";

        printf $format, $bind_energy, $kept;
    }
}
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If you find the variable $format approach unclear, you can achieve the same result by just using multiple printfs and an if conditional:

#!/usr/bin/perl
use strict;
use warnings;

my $best = {1 =>[1,2]};
my $kept_best = {1 =>[1]};

my $width = 10;
my $precision = 5;
my $format = "\%${width}.${precision}f ";

printf "%-${width}s %-${width}s\n", "BEST", "SELECTED BEST";
foreach my $value (sort keys %$best){
    foreach my $bind_energy (@{$best->{$value}}){
        printf $format, $bind_energy;
        
        my $kept = shift @{$kept_best->{$value}};
        printf $format, $kept if defined $kept;
        
        print "\n";
    }
}
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TIMTOWTDI.