Nice work Marcin, that's how I would of approached it with a pre-made board. Using a vacuum bag and a composite vacuum you can easily get close to 30inHg. Before I picked up the Onda Longa, I had planned to make my own board out of maple and fiberglass. This would allow a custom compartment to offset the battery height like you just did. Adding sheets of CF and Kevlar goes a long way in making it stiffer and thinner. Since then, I have gone the route of bigger wheels, due to the rough road conditions we have here. This added height makes it easy for me to secure packs to the bottom. Since the board is so big, stealth hasn't been one of my concerns.
CNC is also one of my hobbies, you should check out my website.