I tested adding a new feature class to a registered geodatabase in ArcGIS Enterprise 10.8.1 which already had 50 feature classes and the sync only took around 30 seconds. ArcGIS Server and the DB are on the same machine so there's zero latency, but that's still a significant difference in processing time.
A couple of things to check...
If any of the datasets that you're syncing participate in relationship classes, then the related data must also be synchronized as well, so the connecting user requires view privileges on both (I think I've seen this problem produce your error before).
Also, check the documentation field size in the GDB_Items table in your database using this query:
SELECT [ObjectID]
,[Name]
,DATALENGTH([Documentation])/1000 as DocumentSize_KB
,[Documentation]
,[ItemInfo]
,[Shape]
,[ContingentValues]
FROM [DATABASE].[sde].[GDB_ITEMS]
ORDER BY DATALENGTH([Documentation]) desc
Whenever you run tools against feature classes or geodatabases, the execution of that tool creates a lineage record in the XML:
This article describes how to delete the geoprocessing history from both the workspace and feature class XML - How To: Delete geoprocessing history from a geodatabase (esri.com)
XML around 1Mb can cause a little bit of slowness, anything over 10Mb can cause serious problems. I haven't encountered any scenarios where I've seen this directly affect the layer syncing process, but it is looking at the metadata (which comes from this documentation XML) so it could potentially be a factor.