I’ve answered a similar Question ( Inherit plugin settings to new site in Multisite ).
And, if understood correctly, “auto setup their unique preferences” would be a matter of adding/updating a custom plugin options array into wp_options
table.
So, following the WP-Pagenavi example. After the plugin auto install/activate run something like:
(not tested)
function set_my_plugin_options(){
$defaults = array(
'pages_text' => 'Page %CURRENT_PAGE% of %TOTAL_PAGES%',
'current_text' => '%PAGE_NUMBER%',
'page_text' => '%PAGE_NUMBER%',
'first_text' => '« First',
'last_text' => 'Last »',
'prev_text' => '«',
'next_text' => '»',
'dotleft_text' => '...',
'dotright_text' => '...',
'num_pages' => 5,
'num_larger_page_numbers' => 3,
'larger_page_numbers_multiple' => 10,
'always_show' =>,
'use_pagenavi_css' => 1,
'style' => 1
);
update_option( 'pagenavi_options', $defaults );
}