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First I created a new table in the physical layer, with its proper name, let's say F2. After adding its fields I added the following join: ORIGINAL_FACT_TABLE.COMMISSION_LINE_ID = F2.COMMISSION_LINE_ID.
The I dragged the entire table F2 in the BMM and created the logical join just like before.
So do I need to add the source table of my new F2 to the source table of the original fact table?
Delete the join in BMM layer and column mappings, just follow as I said earlier.
I would treat the new table as fact extension. Unlike dimension extensions(these go with LTS) fact tables need to map physically.
Just in case if you want to go with your own way as you've done-> You need to add all those dimension keys in new fact(ie F2) treat as 2nd LTS, this would result more or less as you do for aggregate tables.
Hope this helps, pls mark if it does