Ah, of course. That distinction becomes important so rarely for me that it's easy to forget. So, to remove the referencing, and make it show up "as expected", I just add zero to each item, and I get what I expect:

use strict;
use warnings;

sub func {
    print $_, ' ' for @_;
    print "\n";
    $_[2];
}

my $i = 3;
my $rv = func(0+$i, 0+ ++$i, 0+$i+2);
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And now I get my "3 4 6" - and everything makes sense again. See? I knew I did something wrong ;)