I’m using a similar configuration for my Plex Server (Windows Server 2016) with 20+ TB in the cloud.
What I have found to work best is to let Plex operate using NetDrive configured so that it always retrieves the file list from the server and to use the web interface for each of the respective storage providers to upload media from my workstation.
Netdrive aside, if you’re writing files from your plex server while attempting to play media from the same server, you’re going to have performance hits in the playback. Let your media server be, just that, a media server and use NetDrive, or the web interface, on a separate workstaton to do the upload work.