What I don't see how to do is create a Y1 object. that contains a X1 and an Array of X2 objects.

Weak containment with pointers/references is the standard practice, using scalars for single objects and arrayrefs for multiple objects. Roughly for instance:

package Y1;

sub new { 
  ...
  $self->{X1} = X1->new();
  $self->{MANY_X2} = [ X2->new(), X2->new() ];
  ...
}

package main;

my $obj = Y1->new();
print $obj->{X1}->{X1prop};
print $obj->{MANY_X2}->[1]->{X2prop};
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