Secure communication is crucial in many emerging systems enabled by unmanned aerial vehicle (UAV) communication networks. To protect legitimate communication in a chaotic UAV environment, where both eavesdropping and jamming become straightforward from multiple adversaries with line-of-sight signal propagation, a new reliable and integrated physical layer security mechanism is proposed in this paper for a massive multiple-input-multiple-output (MIMO) UAV system. Particularly, a physical layer fingerprint, also called a tag, is first embedded into each message for authentication purpose. We then propose to reuse the tag additionally as a reference to encode each message to ensure secrecy for confidentiality enhancement at a low cost. Specifically, we create a new dual-reference symmetric tag generation mechanism by inputting an encoding-insensitive feature of plaintext along with the key into a hash function. At a legitimate receiver, an expected tag, reliable for decoding, can be symmetrically regenerated based on the received ciphertext, and authentication can be performed by comparing the regenerated reference tag to the received tag. However, an illegitimate receiver can only receive the fuzzy tag which can not be used to decode the received message. Additionally, we introduce artificial noise (AN) to degrade eavesdropping to further decrease message leakage. To verify the efficiency of our proposed tag-based encoding (TBE) scheme, we formulate two optimization problems including ergodic sum secrecy rate maximization and authentication fail probability minimization. The power allocation solutions are derived by difference-of-convex (DC) programming and the Lagrange method, respectively. The simulation results demonstrate the superior performance of the proposed TBE approach compared to the prior AN-aided tag embedding scheme.