A revenue import is mapped with only Lookup ID and the Revenue Update batch is also mapped to only Lookup ID. When importing the batch it will match all IDs including alternate IDs
This is the way this is set up to work and the way it finds Lookup IDs in the system. It will pull in any Lookup IDs associated with the constituent including alternate IDs even if its multiples. The ONLY way for you to avoid the errors your encountering at this time is you’re going to have to replace Lookup ID on the import file with the GUID. The GUID is unique enough that it will only pull the constituent and not all the extra.