You added a feature, in Litium version 8.12: Ability for administrator to set customer number for organization and person. In this feature you added a validation that makes it impossible for a Person and Organization to have the same Id.
Your reason for adding this validation is:
"The reason this rule was added was that it was confusing for users that was working in BO if person and organizations was having the same customer number, specifically when buyer called customer service and customer service was getting multiple entries with the same customer number"
I understand your reason, but since your data model does not have this constraint it's confusing having it forced in the platform - specially when there is no clear documentation on the validation rules - and the validations might not suite all customers.
My suggestion is that you make these validation rules optional in some way, since you said you won't remove them.