`Job_Id` is included and indexed because it is used in JOIN condition. 

`Run_date, Run_time` are included because they are used in the expression of the most inner subquery condition, and `Run_date` is also included into the output list, so they not needed to be sorted. Their values should be extracted from the index, and server don't need to access the table body while executing this query.

I don't know why `Instance_id` is included - it is not used in the query. Maybe the same index also improves some another query where this column is used?

PS. You use `TOP 10000` but there is no ORDER BY clause... do you really need ANY 10k rows from all selected by the query?

> To my understanding, columns in a where clause should be present in the index key for seeks to be possible.

You do not use these columns directly, they are used in the expression. This prevents any index seek, onky index scan is possible. So they may be either indexed or included. But when they're indexed then the server must perform additional and unneeded work while changing the data because of additional sorting steps.