Hello,
As such there will be no issues in Project Planing, budgeting, and finally settlement .
It is possible to have different business areas in a single project (but on different WBSE) based on the responsibility especially to handle the transfer price functionality.
You can also use subproject functionality to control the budget for different budget areas.
In ECC 6, Profit Centers are used where as earlier it was business area.
Regards
Shubham