You'd need one of the design team to be certain of the original reason, but the usual reason for inboard ailerons are to reduce torsion moments on the wing structure, allowing a less stiff (and thus lighter) wing. IIRC the original use would be the F100.
Moving the ailerons away from the tips also reduces flutter risks.
Many airliners use spoilers rather than or in addition to ailerons for roll control (also to reduce torsion moments on the wing structure). In some cases the spoilers and ailerons are scheduled at different points in the flight envelope while in other the spoilers are the primary controls and the ailerons just provide "feel" (concept originally developed for the XF-11, I believe).
Remember that most airliners of this lineage have torsionally "flexible" wings (to reduce weight) and use the podded engines as mass-dampers to mitigate the flexibility.If an aeroplane has reduced wing structure weight in this way you wouldn't want to add further flap area outboard, as that would add further steady-state torsion loads which would require a stiffer, heavier wing again.
It's all about finding the optimum trade-off between performance and weight.