would this still work for more than 2 strings

As long as the ambiguous bases are in distinct positions, yes.

In the general case, you can then write:

my @s = (
    "AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA",
    "ACGTACTAGWCTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGMCATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGACATCTACAGACTCATRAGCAGCATATTTA",
    # ...
);

my $m = shift @s;
for my $s (@s) {
    my $m_ = $m;  $m_ =~ tr/ACGT/\0/c;
    my $s_ = $s;  $s_ =~ tr/ACGT/\0/c;
    $m = $m ^ $m_ ^ $s ^ $s_ | $m_ & $s_;  
}
say $m;   # AYGTACTAGWCTACAGACTACAGMCATCTACAGACTCATRAGCAGCATATTKA
             ^       ^             ^               ^           ^
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(P.S., sorry — meant to reply to garyboyd... )