Playing with google image search turns up a nice big rectangle.
I would buy a sheet of metal to cover it.
I would figure out what all is underneath that so you know how you want to add hinges at the back or sides, and it is up to you on how you want to lock it.
Simple as having a hasp and a padlock or set it up with a keyed lock built into it.
To some extent you could hinge the lid in the middle so it folds back as well, maybe you don't need the whole lid to open.
I did not sit and look for rav4 discussions but I expect more than a few folks have had this idea before and might have been silly enough to post it on the net.
If that does not work, I would find a metal box with a lid design you like. If it is too tall, no worries. Cut the bottom off the sucker.
As long as you are bolting it down your "lockbox" does not really need its own floor.
Something as simple as a beefed up briefcase might work, I did not really sit down and figure out what size stuff you can actually fit and mess with.
I like some tuffy stuff but you tend to pay for it dearly.
Then again, I could see where it might be worth it to some people.
But I think a big piece of aluminum diamond plate or something similar and hinge it and figure out how you want to make it lock would work.
Put a piece of carpet or floor mat or something over it, or glue it to it even.