Create Lookup Filter in lightning Screen Flow

 Lookup filter does not apply on Screen Flow, there is a workaround for this 

Create a Record Choice set based on filter criteria as below 

Step 2: Create a separate screen with the Picklist component and add the above choice set.

Then you will see the Filter record and you can select any record from the list and selected record Id assigned to SelectedSaleOrg (text variable).

It is working fine for me.