Microsoft embeds Flash Player in IE on Windows 8.x and above. As such, they consider the Flash Player ActiveX files to be system files and advise against deleting them, including the \Macromed\Flash directory. I have heard of a few people delete the ActiveX files and the directory (using some 3rd party unlocker utility to unlock the directory/files, since Microsoft locks these files on Windows 8.x) and the result was that they ended up having to re-install the OS to fix the problem they created.
For your other questions:
1 - Since Microsoft embeds Flash Player ActiveX in Windows 8, the standalone Flash Player ActiveX installer (EXE or MSI) does NOT execute on Windows 8.x machine. NPAPI and PPAPI installer do write to that folder.
2 - NPAPI and PPAPI files live in the same directory: \Windows\System32\Macromed\Flash. If 64-bit OS, also live at \Windows\SysWow64\Macromed\Flash.
3 - All versions of IE on Windows 8.x use the ActiveX player embedded by Microsoft. The embedded version cannot be deleted and the standalone ActiveX installer will not execute on Windows 8.x systems.
4 - If you manually delete the ActiveX installer, or the Macromed\Flash directory you'll most likely need to end up re-installing the OS. None of the ActiveX standalone installers will execute on Windows 8.x. Microsoft considers the embedded Flash Player ActiveX files to be system files and does not want users deleting them due to the problems it creates when doing so. This is why Adobe recommends against deleting the ActiveX files and the \Macromed\Flash directory on Windows 8.x.
Hope this answers your questions.