I had the chance and did the same thing again as last time: the executable of MSFS is installed on the same HDD as Windows is as well as all standard packages and market place content. Freewares and other third party packages are installed on another disk and linked with addon linker.
I personally think the discussion on what to install where is a bit of snake oil - if you have two fast M.2 SSDs these won’t be a limiting factor imho 
The only thing which could play a role is caching being done by the OS and being consumed by MSFS (like streaming of data), however the most limiting factor here is the connection speed to the server and not the internals of your system (Mbit/s vs. Gigabit/s).