I guess that recommendation is to avoid collisions with other apps using those same shares and potentially messing things up (e.g. changing file names, reorganizing files…). Personally I’ve been using the standard folders for quite some time (years) without issue. That being said I’ve also never allowed any other apps to work with those shares… so no risk of collisions.
As it is, Synology didn’t create any of its own shares. Now, a new problem. I installed Plex, not allowing it to run after installation. When I created a Share (called DMMedia), I found only myself, guest, and Admin. I had to go back out and add in Plex, which (whom?) I named “plex” (all lower-case like shown in the step by step installation doc for Synology. I went into File Station and created folders in my DMMedia shared folder. Mvvies, Movies, Silent, Soundies, Music, etc.
I then started Plex Server, and wanted to start adding libraries. None of the folders like Soundies etc show up.
After running the Plex Media Server on your Synology NAS with DSM 7, you should be able to set/pick permissions for its standard user (PlexMediaServer).