Actually KiCad supports SMD pads on inner layers, but not in the level of UI when footprints are created. You can manually edit the footprint file or the board file and just change the layer of the pad and the non-pad copper shape. (Remember to remove the mask and paste layers from the pads.)
(fp_rect (start -1 -5.75) (end 1 7.75)
(stroke (width 0.2) (type solid)) (fill solid) (layer "In1.Cu") (tstamp 2b0cf023-cd8f-4153-a15b-d75eaa108009))
(pad "4" smd roundrect (at -0.18 7.58) (size 2.286 1.524) (layers "In1.Cu") (roundrect_rratio 0.25)
(thermal_bridge_angle 45) (tstamp a4d99cc6-ee1e-4cf3-944e-6062ff8be303))