802.1X authenticates the port and as long as it is authenticated it participates in the network. Inserted or even modified frames by an otherwise transparent network device cannot be detected.
802.1X has had some serious attack vectors from the start and can only be regarded as a "better than nothing" approach. If you want serious port security you'll need 802.1AE aka MACsec.
Another approach (thx Ricky) is to forgo port-level security completely and instead rely on VPN connections you build on top of your physical network, basically moving the security up the stack. While this can be made very secure and backward compatible with just about any infrastructure, it may introduce bottlenecks at the VPN router(s) and their links.