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This is exactly how rooting is done. "Root" is granting write access to the root directory of a running OS. It is utterly unrelated to flashing.
You may flash something to gain root access, or flash a pre-rooted image, but root is still a function of a running OS, it's logically other same as Administrator rights in Windows.
As for how GServices being intricately tied into a compiled ROM, believe what you want - rip out the GServices files with 3C Toolbox, and you'll find out exactly how tightly bound they are to the image. I'd be surprised if it doesn't boot loop (I've done this myself, even simply freezing them can boot loop a device).
Because... Integrated dependencies. Android isn't just "some other piece of software", it's an OS, like Linux and Windows (to be accurate, it's a Linux Kernel with Android as both the API layer and shell). When Google-less Roms are compiled, they do so with none of the Google services dependences. Even those Roms, if you flash something like MicroG, if you then delete those files, you get a boot loop because it's added those dependencies to the ROM.
Ask the folks at Lineage or DivestOS.