There'll be a few templates to change, I think, for those places which link directly to admin.php, but the change to the routing formatter itself can be done without changing any core files in XF2.
Just add the following to your src/config.php file:
PHP:
$c['router.admin.formatter'] = $c->wrap(function($route, $queryString)
{
$suffix = $route . (strlen($queryString) ? '&' . $queryString : '');
return strlen($suffix) ? 'not_admin.php?' . $suffix : 'not_admin.php';
});
Replace
not_admin.php
with whichever name you have renamed admin.php to.