Your approach is fine. You can program the BLE USB Dongle with a custom central/client firmware which looks for the specific data from a peripheral/server device ( for example characteristics UUID) and based on this establishes a BLE connection.
Please have a look at below link which has two examples both for Central and Peripheral device. Here the central device looks for a specific characteristics UUID for filtering a particular peripheral device. The central project can be flashed into the dongle.