It looks like a good start for a bench. I have never been a big fan of using rods through workbench tops. If you tighten them enough to prevent splitting at the ends then you will compress the wood in the rod area when expansion occurs due to humidity changes. Subsequent top shrinkage will result in a loose fit which negates the original purpose of the rods. Just out of curiosity, how were you planning on drilling the holes for the rods anyway? Most of the tops I have seen that used rods had the holes drilled prior to glue-up and the rods were used as part of the clamping process. Just be sure to fasten the top to the base so that the top can expand/contract with humidity. Slotted screw holes in the base rails are good for that. Be sure to equally finish all surfaces (especially the ends) of the top to equalize and limit humidity gain/loss.
The vise only needs to be inset enough to clear the hardware from the bench face after you have done your final top shaping. You could allow enough extra to allow for some future re-surfacing of the edge face for future rehab, maybe 1/8 inch or so. Just remember that the further you inset the vise then the shallower the vise can clamp. Wood faces added to the movable portion of the vise are normally a little wider than the vise hardware. decide what length of face you want to add and place the vise so that the wood face edge is even with the finished top edge to facilitate operations at the bench end. that will show you where to attach the vise hardware on the underside of the top. Properly installed lag screws or bolts should be sufficient for mounting the vise and no further bracing should be necessary as long as you use proper woodworking techniques. I don’t recommend mortising in a vise with a sledge hammer.
Theoretically you could just flatten an area on the underside to accommodate the clamp hardware but it would benefit you to flatten he whole underside to facilitate mounting the top to the base or any other operations. It need not be as flat as the bench top but should be basically flat and parallel to the top surface. Have fun.