Having Sharepoint on a different Collation than the system Databases?
Having a different default collation for the instance than for the SharePoint DB is not necessarily a problem. The main thing to ensure is that the SharePoint DB is set to the correct collation for SharePoint, which is Latin1_General_CI_AS_KS_WS, and which you have done.

You quoted a section from Supportability regarding SQL collation for SharePoint Databases and TempDB (in the future, when you quote something, you really need to attribute the source) which clearly states that SharePoint does indeed "support any CI collation for the SQL instance (for master, tempdb databases)". Hence, Latin1_General_CI_AS being case-insensitive, is supported.

The only other guidance I have found, and which makes sense, even outside of SharePoint, is this:

SharePoint SQL Collation - Best practice

The main point expressed there is that if you have more running on this instance of SQL Server than SharePoint, then sure, use whatever collation makes sense. Else, it is easier to just have it match between SharePoint and the system DBs.