Yes, we have been thinking about that. Actually, we envision a larger 'character data and tree(s)' object ("CDAT"). The idea is that the CDAT object has slots for trees, matrices and taxa, that each specify to the CDAT object which other objects (by UID) they're watching and what actions to take, e.g.:

my $matrix_id = $cdat->add_matrix( $matrix );
my $tree_id   = $cdat->add_tree( $tree );
$cdat->add_handler(
    'listener'   => $tree_id,
    'observable' => $matrix_id,
    'handler'    => \&handler,
);
sub handler {
    my ( $listener, $observable, $method, @args ) = @_;
    # $method is called on $observable,
    # but supervisor $cdat creates an 
    # indirection layer to notify listeners
    print "$method '@args'" # prints "set_name 'New matrix'"
}
$matrix->set_name( 'New matrix' );
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...where the $tree, $taxon and $matrix objects have a way of notifying the $cdat object to trigger the handlers specified for their respective ids when they change state.

In the example, the $tree is watching the $matrix, and so when a method call is placed on the matrix, the tree can check what has changed and act accordingly.

I foresee problems with deep recursion when subsequent actions are triggered on the tree, which might in turn be watched by the matrix. How would you deal with that?