How to design a table for reconciliation
It depends on amount of data and how it will be used. You can have one table for with flag for intraday/COB datasets, then queries that would filter on those flags. After that you'll probably use EXCEPT to get unprocessed transactions. Then you need to keep this data for  2-5-7 years. There may be more requirements. It is OK if you have enough capacity and the only use for this table is one-off reconciliation and then storing data.

However, if you need to run reports on COB data, join it to dimensions, do more reconciliation, enrich with more attributes, send to downstream systems, then you would go for a separate table.