A semiconductor device has a first conductive layer formed over a first substrate. A second conductive layer is formed over a second substrate. A first semiconductor die is mounted to the first substrate and electrically connected to the first conductive layer. A second semiconductor die is mounted to the second substrate and electrically connected to the second conductive layer. The first semiconductor die is mounted over the second semiconductor die. An encapsulant is deposited over the first and second semiconductor die and the first and second substrates. A conductive interconnect structure is formed through the encapsulant to electrically connect the first and second semiconductor die to the second surface of the semiconductor device. Forming the conductive interconnect structure includes forming a plurality of conductive vias through the encapsulant and the first substrate outside a footprint of the first and second semiconductor die.