Recent revolutionary advancements in the services as observed with the use cases of Industry 5.0, consumer electronics 2.0/smart devices 2.0, digital healthcare ecosystem, Internet-of-Things (IoT), advanced digital finance/currency, and Non-Terrestrial Network (NTN) expansion, to name a few, have resulted in a spectacular growth in the number of wireless-connected devices. Subsequently, this has drastically increased the demands for network capacity, channel capacity, reliability, privacy, and security provisions. Despite that, the 5 th Generation (5G) of wireless communication networks has introduced various innovative services such as Ultra-Reliable Low Latency Communication (URLLCs), Massive Machine Type Communication (mMTCs), and Enhanced Mobile Broadband (eMBB). These services only support isolated operations and the requisite reliable service delivery remains a challenge. The Beyond 5G (B5G)/6 th Generation (6G) wireless networks aim at simultaneously providing multiple integrated services through intelligent network operations with ultra-high speed and reliability supporting integrated NTN and terrestrial networks. However, the prospect of such an extensively connected decentralized 3D wireless network also foresees security concerns, underscoring the necessity for seamless and infrastructurefree (decentralized) security solutions. The conventional security mechanisms are considered inadequate to ensure the security provisions of such extensive, decentralized, and heterogeneous networks. Physical Layer Security (PLS) is a promising technique to extend seamless and infrastructure-less security solutions, ensuring the availability, confidentiality, and integrity of legitimate transmissions. This paper provides a comprehensive overview with tutorials and presents the state-of-the-art of PLS, focusing mainly on NTN wireless communications. Furthermore, current research challenges, open issues, and future research directions are also thoroughly discussed in an amalgamation of various emerging 6G technologies. Finally, we provide an overview of implementation challenges in NTN and potential solutions to support the standardization progression of NTN in upcoming releases of 3 rd Generation Partnership Project (3GPP).