Query Custom Post by taxonomy multiple categories

This should give you an OR relationship:

$args['tax_query'] = array(
  array(
    'taxonomy'  => 'category',
    'field'  => 'id',
    'terms'  => array(1,2),
    'operator' => 'IN'
  )
);

As would this:

$args['tax_query'] = array(
  'relation' => 'OR',
  array(
    'taxonomy'  => 'project-type',
    'field'  => 'id',
    'terms'  => array(1)
  ),
  array(
    'taxonomy'  => 'project-type',
    'field'  => 'id',
    'terms'  => array(2)
  )
);

Be aware that that will become increasingly inefficient as you add more terms. It should perform tolerably with just two. The first version is neater and probably performs better in general, unless you need to search by multiple taxonomies.