My reading of the Net::SSH::Perl documentation says that identity_files => [$rsa_file] is for the id_rsa or similar identity , not for your known hosts file -- ie, the key sent to the remote server for authentication. It mentions UserKnownHostsFile in the options section, so that implies that the following might be what you want (untested):

use Net::SSH::Perl;

my $keyfile='~/.ssh/known_hosts';
my $ssh = Net::SSH::Perl->new( $host, options => ["UserKnownHostsFile 
+$keyfile"] );
[download]

If I run Data::Dump::dd on $ssh , it will show the default path to known_hosts2 if I don't have that options parameter, but shows the new path I indicate if I do have that parameter, so I think it's right. (But I don't have a known-working connection for Net::SSH::Perl to test, since I've never used that module and only installed it to look into this question, and couldn't get a connection working in the 5 min I allocated, so I cannot tell you that it will for-sure work.)

---

update: a few hours later, the following SSCCE works for me

#!perl

use 5.012; # strict, //
use warnings;
use autodie;

my $hostname = "obfuscated";
my $username = "obfuscated";
my $known_hosts = '/obfuscated/.ssh/known_hosts';
my ($id_rsa, $id_ecdsa, $id_ed25519) = map '/obfuscated/.ssh/'.$_, qw/
+id_rsa id_ecdsa id_ed25519/;

use Net::SSH::Perl;
use Data::Dump;
my %options = (
    # debug => 1,                       # set this one to help with de
+bug
    protocol => 2,                      # ssh2
    interactive => 1,                   # ask for password if somethin
+g goes wrong
    strict_host_key_checking => 'yes',  # makes sure it actually check
+s known hosts
    options => [
        "UserKnownHostsFile $known_hosts",                  # defines 
+the user path/name for known_hosts
    ],
    identity_files => [$id_rsa, $id_ed25519, $id_ecdsa],    # defines 
+the possible identity_file path strings
);

my $ssh = Net::SSH::Perl::->new($hostname, %options) or die "create ss
+h: $!";
#dd $ssh;                               # use this when debugging the 
+various %options
$ssh->login($username) or die "login: $!";  # using id_rsa identificat
+ion, at default id_rsa location, or ask for pw if it fails
print map { $_//"<undef>\n", "\n----\n"} $ssh->cmd('pwd');
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I tried with known_hosts and known_hosts2 and even the made-up known_hosts3 and they all worked -- if they didn't exist, it would prompt if I wanted to save the host key; if it did exist already, it would use that previously-saved host key.