Actually your theme footer option is brilliant good where has option to put how many column, but it might be little problematic.
Understand your theme footer widget area is depending on how many widgets have been used, but it would have problem when below situation:
A1 + A2, B1+B2, C , D (4 column)
A,B,C,D is column, 1 and 2 are within same column area.
If based on your theme logic, sure it will be:
A1, A2, B1, B2, C1, C2 where be 3 column
Hopefully have option to control which widget under which area. TQ