Discard the "pos" part of %pos2base2bin, sort the keys of %base2bin, print those on the first line and print a hash slice on the second.

use 5.026;
use warnings;

my %pos2base2bin = (
   '315' => {
              '8' => 0
            },
   '329' => {
              '6' => 0
            },
   '352' => {
              '5' => 0
            },
   '390' => {
              '1' => 0
            },
   '280' => {
              '7' => 1
            },
   '360' => {
              '9' => 0
            },
   '349' => {
              '4' => 0
            },
   '305' => {
              '10' => 0
            },
   '380' => {
              '3' => 1
            },
   '251' => {
              '2' => 0
            }
   );

my %base2bin = map { %{ $_ } } values %pos2base2bin;
my @order    = sort { $a <=> $b } keys %base2bin;

say qq{sample\t}, join qq{\t}, @order;
say qq{file1\t},  join qq{\t}, @base2bin{ @order };
[download]

Produces:-

sample  1       2       3       4       5       6       7       8     
+  9       10
file1   0       0       1       0       0       0       1       0     
+  0       0
[download]

I hope this is of interest.