I think some of this might just be misunderstanding some of what normal rabbit behavior is, as well as the body language your rabbit is showing. Your rabbit being flopped down relaxing out in the open, is not insignificant. It shows a sign of comfort in her living environment, as well as a great deal of trust in you. A scared or traumatized untrusting rabbit, would not have that body posture or be laying out in the open like that. A rabbit in this state would be more than likely hiding most of the time, in dark small spaces if possible, and would not be laying down like that, even while sleeping.
As for her other behaviors, some rabbits aren't big into exploring. That doesn't necessarily indicate any sort of problem with them, and that lack of exploring doesn't mean they aren't content. It can just be a normal personality trait, as well as a rabbit respecting territorial boundaries (not wanting to encroach on what she sees as 'your territory'). Though rabbits that have lived for years in a cage, can sometimes be slower to want to explore when given the opportunity.
With this it's just a matter of patience and building that trust at their pace. But they can still be a perfectly happy bun in the space they're in, even though they're restricting what they see as their available territory. Sometimes they just need time to start seeing 'your territory ' as space they're allowed in. And we know with rabbits that some, no matter their background and life previously, can be very slow to get used to changes and build trust. It's just their personality.
Neither does the lack of playing with toys mean a rabbit isn't perfectly happy. In fact many rabbits are completely uninterested in typical 'toys'. Most of my rabbits haven't been. And it may just be that you haven't found the type of activity that your bun would enjoy. What each rabbit enjoys doing is a very individual thing. I always had the best luck providing things that were in line with a rabbits natural behavior; like digging boxes, newspaper to shred, fleece blanket to rearrange (simulate digging and moving dirt), and rabbit safe branches and leaves to chew up.
https://wabbitwiki.com/wiki/Toys_and_games
With petting and head rubs, I've had rabbits that didn't want me petting them at all, even though they had a perfectly loved and happy life since raising them from birth. It had nothing to do with upbringing, but everything to do with individual personalities. But sometimes it also has to do with how they're being petted and when.
Some rabbits will only accept being petted on a certain spot, usually the forehead, as this is where rabbits most often groom each other. Some rabbits hate being petted anywhere else on their body. The timing can also be important. Some rabbits love to get head rubs whenever you're offering, some will only allow it when they approach you and request it(eg nose nudge, head down, head pushed under your hand), some will let you pet while they're eating, and some will only accept petting while they're relaxed and resting. So it's important to time it right for a particularly fussy rabbit. But this is only the case if you have developed a certain level of trust with them first.
Not wanting to be held is also very normal rabbit behavior, and is actually the rule more than the exception. As a prey animal, rabbits in general don't like being picked up or held, since this is what would happen to them when caught by a predator in the wild. It's instinctual to them. Most rabbits prefer being on a solid surface while you pet and interact with them. Though some rabbits can learn to get past this by learning they can trust us, even while experiencing something that would normally be against their nature, like being held. For some it can be an almost immediate trust, though for the majority it takes time and patience to build that amount of trust with them.
https://www.rabbitsonline.net/threa...-me-and-biting-my-clothes.96208/#post-1124801
https://www.rabbitsonline.net/threa...g-running-away-hiding-etc.99650/#post-1155926
Though none of this is to say your rabbit doesn't have some trauma and resulting behavior from her previous life. That could certainly be affecting her as well, but I would be inclined to say that it's more likely that her behavior is a combination of both normal rabbit behavior and her past. Understanding this will make it more possible knowing where you can and can't affect change, all with gentle persistence and patience.
What I would suggest is spending as much time sitting with your bun as you can, on the floor at her level if possible. Read, work on your phone or laptop, and just allow her to approach you when she's ready. This is how rabbits form bonds, by time spent being near each other, to be able to learn their place in the hierarchy and gain that trusting relationship. Having a good understanding of rabbit body language will also help you on this journey.
https://rabbitsindoors.weebly.com/bonding-with-your-bunny.html
https://flashsplace.webs.com/bondingwithyourbunny.htm
https://www.rabbitsonline.net/threads/language-of-lagomorphs-is-it-gone-forever.105436/
https://wabbitwiki.com/wiki/Understanding_your_rabbit
