Keep looking for a another house with a three car garage.
In the Phoenix area a garage is worth about $8-10K, which works out to about $20 a square foot. You can't build anything for $20 a foot and you can finance the garage in the mortgage. I would imagine the excavation/grading alone costing $8-10K for your subterranean space, assuming no rock or caliche.
Setting aside the flooding potential issues for the moment, I'd talk to an appraiser first. This looks like an opportunity to spend a wad of money and, best case, get little or nothing for it at resale.
I believe to be considered livable area, the space has to be at the same grade as the house. I question the viability of converting it into a guesthouse at a later date. Even if you could, I think a guest house whose roof line was 6' above grade would be a white elephant at resale.
If you're committed to a stand-alone structure, a better idea might be to get an approval for a guest house up front, but design it such that you could use it for your motorcycle hobby now and convert the interior to livable space when you want to sell the property. But even if you're successful with this, guest houses typically on get 50% of the square foot price of the house.
PS - the OP's comments about the HOA and limiting the height to 6': HOA's typically don't require approval of structures that can't be seen in the backyard. If you go over 6' you'd likely need to get HOA approval (if there is one)