I'm using Drive to keep my NAS'es in sync with each other.
Versioning is disabled in Drive.
The sync is working fine, does anyone know why these "System rotated the earliest version of ...." message popup everywhere in the logs...?

the red cross is means - deleted, in your case deleted last possible version
but you don't have Versioning enabled. Hm.

check all the Teams/Home folders in Drive console for Versioning. Just to be sure.
check - where you can find these "versioned" files in your NAS. Then try to select one of the file in File Station, left click (win), then click to Synology Drive console. When you see it, you have enabled versioning.

Logically you can think of versioning being disabled is the same as version history of 1 (the latest). By implementing it this way you don't have the have two process flows, just one that checks max version parameter and deletes ones that exceed it (according to the rotation policy).

As such, if you didn't have a special logging rule to say 'if max version parameter = 1' then don't log' you will log all deletions whether the GUI says versioning disabled or max versions >1.