Created by Microsoft as the foundation of its .NET technology, the Common Language Infrastructure (CLI) is an ECMA standard (ECMA-335) that allows app
"System environments" means things like Linux, Windows x86, Windows x64, etc. Notice how they use the term "architecture" interchangeably at the end of the paragraph.
A native C++ program is one where you take standard (ANSI/ISO) C++ and you compile it into a .exe. Usually you will be compiling this for a specific environment, e.g. Windows x86, in which case it could not run under Linux and would run under the WoW64 emulation layer on Windows x64. Notably, this code runs directly on the machine.
C++/CLI is a different programming language than standard C++. It, just like C# or VB.NET, runs on top of Microsoft's Common Language Interface. This means it has access to all those nice things in the paragraph you quoted, like the base class library and compilation to IL which allows it to be run on different architectures. But, just like C# and VB.NET, it does not run natively on the machine. It requires the installation of the .NET Framework; part of the .NET Framework's job is translating C++/CLI programs into native programs, which means they have much less direct access to the machine.