If you set the prototype of your mock sub before replacing the original one, that should get rid of the warning, try commenting out the set_prototype call in the following and you should get the "Prototype mismatch" warning back:

use warnings;
use strict;
use Scalar::Util qw/set_prototype/;

sub foo ($$$) { print "foo(@_)\n" }

foo(1,2,3);  # prints "foo(1 2 3)"
{
        my $name = "foo";
        my $sub = sub { print "bar(@_)\n" };
        set_prototype(\&$sub,prototype($name));
        #use Devel::Peek; Dump($sub);
        no strict 'refs';
        no warnings 'redefine';
        *$name = $sub;
}
foo(4,5,6);  # prints "bar(4 5 6)"
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By the way, in the code you showed, you're disabling strict 'refs' for a fairly large block of code.