How to set body field display programmatically on node type install?
You can access and alter the view mode configuration via field_bundle_settings(), (which is basically a shortcut to variable_get and variable_set):

$bundle = 'my_node_type';
$bundle_settings = field_bundle_settings('node', $bundle);
$bundle_settings['view_modes']['teaser']['custom_settings'] = true;
field_bundle_settings('node', $bundle, $bundle_settings);