Hm. OPENQUERY presumes that the linked server has been set up with the default database to be desired database. Else you have to specify the database in the query inside OPENQUERY.
This is certainly a workable solution as a linked server is essentially an alias. But it does require server-level configuration, which involves someone with server-level permissions. Which can add complexity. Or be perfectly trivial.
In any case, it does not address issues with database.dbo.tbl, that is cross-database queries on the same instance.
I would say that from a T-SQL perspective, synonyms are better. You can say:
CREATE SYNONYM dbo.myremotetable FOR LINKEDSERVER.db.dbo.tbl
CREATE SYNONYM dbo.otherdbtable FOR db.dbo.tbl
There is still an issue with setting up the synonyms, which you may have to do dynamically for each downlevel environment.
It is possible that there is a better solution inside SSIS, but I don't know SSIS, so I cannot answer that part.
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