... where it effectively ignores dashes....

Preprocess the sequence to get ride of the dashes:

$seq =~ s/-//g; # remove any dashes, first
$seq =~ s/[ATGC]{2}/$&$tag/;
$seq =~ s/$tag[ATGC]{4}/$&$tag/;
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Update: As pointed out, in some circumstances, the desired output can have dashes.

So, add a look-ahead so that only single dashes are removed:

$seq =~ s/-(?!-)//g;
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