I solved the bulk “apply” and “remove” watermark issue by editing image-watermark.php line 112. If you change the priority in which ‘admin_print_scripts’ loads from 20 to something like 80, the js loads below jQuery which allows for the select list insertion.
Go from
add_action( 'admin_print_scripts', array( $this, 'admin_print_scripts' ), 20 );
To
add_action( 'admin_print_scripts', array( $this, 'admin_print_scripts' ), 80 );
This, of course, doesn’t solve the issue with limited amount of images visible by the media library.
