Dealing with different intimacy needs

I'm afraid I can't give you much advice since I know precisely nothing about romantic/sexual relationships, but I do know a little about this stuff outside a romantic/sexual relationship context, and I can definitely give you some nice words.

It's great that you're thinking so carefully about what your girlfriend needs. I suppose that should be standard in any and all relationships, but it's not, so caring enough to pay attention to the extent that you can clearly explain this whole situation actually makes you a bit special. Maybe you feel proud of that, and maybe you feel a little insulted I'm complimenting you on it, but either way it makes you a better person than most people.

So, I guess I kind of have some of the issues your girlfriend has. I have CPTSD (which is like PTSD, but the trauma is basically your entire life), and I've managed to handle it pretty well, but I get really startled if people sneak up on me, and even when I can see someone's about to touch me, I can still get spooked. But I'm also a bit like you because I really like touch.
It's all resulted in this confusing nonsense-mess where my friends usually won't touch me, and that's a little frustrating because I like to be touched, and I can never be entirely at ease with anyone because at any moment some idiot will forget and sneak up on me or the wind will make the door slam or whatever. In that situation, does it help when people ask permission to touch me? For strangers and acquaintances it's good because it shows they're being mindful and they're not going to forget, which puts me at ease, and I don't really want them touching me without warning anyway. But for friends, it makes interactions stilted and it can make me feel kind of isolated, or like I'm being treated like something fragile.

Even though your girlfriend isn't touchy-feely like me, I wouldn't be surprised is she found the asking kind of killed the mood and took away any kind of spontaneity.
Don't get me wrong, though! The asking isn't a bad by any means. A better solution might be to get to the point where she will ask you to give her space if she needs it, but the asking is still a good solution.
In the meantime, definitely keep the asking, but if she seems to prefer the idea of asking for space when she needs it rather than constantly being asked "Is this okay, is this okay, is this okay" then it's something that might be worth exploring. The only problem with that is people often learn not to enforce their boundaries or ask people not to do things because it's 'impolite' or it's a 'buzzkill', so if she has some sort of reluctance related to that, you might need to work on it before you can stop the asking.
A problem I think a lot of people would face in that situation is worrying about offending the other person, so I'd try addressing that by starting with a simple CBT-based technique where you get her to imagine how she would feel if you asked her to give you a little breathing room, then maybe ask her why she'd feel the way she does. She might say something like "I'd be more than happy to. I'd maybe even feel a little bad that I made you feel uncomfortable." then you could say something like "So you wouldn't feel offended or upset with me? Well, that's how I feel when you tell me you need space." or "Wouldn't you say that most people are similar enough that we tend to feel the same things? So, maybe most people would have a similar reaction?"

Just, before you do any of this, keep in mind that I'm not remotely qualified to give out this sort of advice. I'm just some smuck with basically no life experience putting word-vomit on an internet forum. So please be careful which advice you apply, and unceremoniously dump everything that won't be helpful to you (I promise I won't be offended).

Anyway, hopefully there's something useful in all of this. I hope everything goes well with you and your girlfriend, and if it's not going to weird her out, feel free to tell her that an internet weirdo wishes her a speedy and easy recovery with that endometriosis.