I see a couple obvious things:
The hatch cover is too weak to support the AC unit. Simply make a cover or adapter (sheet ply with aluminum covering, self-adhesive foam tape to seal off), place that in the opening, and use longer screws or threaded rod to replace the now-too-short ones.
Next, if you use/build the adapter, maybe set it up so that a couple hold-down latches can be built in....SOMEONE out there makes them, I've seen similar latches in hardware stores (National Hardware brand?). Then if you need the roof exit in case of a rollover, you unlatch the AC, drop it off, and bail out.
The tool storage is nice, but where do I put the bed?