I think it was a good call to open a support case. I don't think it is likely that someone here in the forum will know the solution.
Coming from the SQL Server side, I don't know anything about SMS. The most likely explanation is that there is a query with a bad execution plan that runs longer that your patience allows. In this case, the SQL Server team may be looking at the MCM people and tell them to rewrite the query, and the MCM people thinks that there is nothing wrong with their query and SQL Server should get its act together. And for that matter, the MCM might be right in the sense that the issue may be something that SQL Server could do better. And, who knows, is doing better in later versions of SQL Server.
But there could be other reasons as well, like you are hitting a true bug in SQL Server. For which it is not that likely you will get a fix, since SQL 2016 is out of mainstream support.