You can buy it separately from the bundle and link it to your Smart account. When the FTD registers with the FMC (or directly to Cisco smart license cloud), you will enable the AnyConnect Plus or Apex option. This will assign licenses from your smart license to the device.
On a side note, I would recommend getting the AnyConnect Plus/Apex depending on your use case. This can be shared among multiple devices and is cheaper than the VPN Only license last I checked.
