If you have examples of the system generating invalid joins, we would like to know about that. I do know that sometimes when you join the Order to the Customer table, it will join the BTCustomer instead of the Customer number. But there is also a combo box asking you which of the two joins you want to use.
Many times, we are finding that people create inefficient joins. for example they leave out the join to the COMPANY field, which makes SQL work harder to get to the data you want. Our joins should include the full key to get to the data.