You need to change your tree from

my $tree = {

arr => {
  elem => [
    {
      mod => 'mstring1',
      rp  => 'rstring1',
      subarr => {
        subelem => [
          {content=>'...'}, {content=>'...'},
        ]
      }
    },
    {
      mod => 'mstring2',
      rp  => 'rstring2',
      subarr => {
        subelem => [
          {content=>'...'}, {content=>'...'},
        ]
      }
    },
  ],
}

};
[download]

to

my $tree = {

arr => {
  elem => [
    {
      mod => { content => 'mstring1' },    <------
      rp  => 'rstring1',
      subarr => {
        subelem => [
          {content=>'...'}, {content=>'...'},
        ]
      }
    },
    {
      mod => { content => 'mstring2' },    <------
      rp  => 'rstring2',
      subarr => {
        subelem => [
          {content=>'...'}, {content=>'...'},
        ]
      }
    },
  ],
}

};
[download]

This can be done programmatically.

You can use ContentKey => ... to specify a name other than "content". I have used _text.

If you're creating the tree using XMLin, use ForceContent => 1. Here's a round-trip example:

use strict;
use warnings;

use Data::Dumper qw( Dumper );
use XML::Simple  qw( );

local $XML::Simple::PREFERRED_PARSER = 'XML::Parser';

my $xs = XML::Simple->new(
   ForceArray   => [qw( elem subelem )],
   ForceContent => 1,
   #ContentKey  => '_text',
   KeyAttr      => {}, 
   KeepRoot     => 1,
);

my $tree = $xs->XMLin(<<'__EOI__');
<arr>
  <elem rp="rstring1">
    <mod>mstring1</mod>
    <subarr>
      <subelem>...</subelem>
      <subelem>...</subelem>
    </subarr>
  </elem>
  <elem rp="rstring2">
    <mod>mstring2</mod>
    <subarr>
      <subelem>...</subelem>
      <subelem>...</subelem>
    </subarr>
  </elem>
</arr>
__EOI__

{
   local $Data::Dumper::Indent = 1;
   print(Dumper($tree));
}

print $xs->XMLout($tree);
[download]

Update: I had originally phrased the reply as if the OP started from XML. Rearranged contents.
Update: Added instructions on how to transform the tree programmatically.