I replaced my folding doors with an Anderson 4000 series storm door and had to build up my bottom step since the door was about 4" too short to fill the doorway. I used layers of plywood to build up the bottom step but slathered up the boards with fiberglass resin to seal out the inevitable water leaks. I had planned to use rot proof PVC boards to build it up but I also had to extend the lower step about 1 1/2" past the edge of the existing step and the PVC isn't as rigid as plywood. The Anderson 4000 doors have a three point latch with a key lock and laminated glass. I'm real happy with ours so far.
I briefly thought about dropping the door down and trimming out the top of the opening, but we would have to duck our heads to avoid hitting the top of the frame.
This picture shows the door hung in the opening but the bottom step unfinished.