Try out this code and see if it works for you, I just cooked it up real quick and haven’t tested it, so it may be way off base, but the concept is there.
$tax_args = array(
'public' => true
);
$taxonomies = get_taxonomies( $tax_args, 'names', 'or' );
$term_args = array(
'fields' => 'ids'
);
$terms = get_terms( $taxonomies, $term_args );
Docs: get_taxonomies()
, get_terms()
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