You've mentioned some great Bond girls, such as Dr. Holly Goodhead who as you put it doesn't need Bond, but we can argue that despite her strength and intelligence was she being undermined by her given surname?
Well, this is a typical disconnect for the series. Holly is arguably the most learned and accomplished of all the Bond girls, but she looks like she walked out of a perfume ad, she has a name that suggests a sex act and she's played by an actress whose range makes Roger Moore look like Olivier. Her spiritual descendant is Christmas Jones, a "nuclear physicist" who looks (and acts) like a blow-up doll.
At some point one has to deal with the fact that the character on the script page -- scientist, super-spy, astronaut, crime boss, computer genius -- is being interpreted by a fullsome ingenue whose chief strength lies in a set of numbers that has nothing to do with IQ. The series is great at paying lip service to equality and women's lib and "strong female characters," but in the end they're all eye candy first. I seem to remember a lot of press around the time of Goldeneye saying Natalya was a "modern woman" who wouldn't spend all her time in a bikini, but I also remember a lot of press photos showing her in exactly that. I lost track of how many leading ladies said at a press conference, "My character isn't the usual bimbo Bond girl; she's Bond's equal." Then we saw the film and learned her character was the biggest airhead in the lot. Eventually this claim was made so often the press conferences felt like "Mad Libs", and 9 times out of 10 they were about as truthful as Broccoli's claim that MR was "Science Fact."
Sometimes I get the distinct impression the series (at least Classic Bond...the Craig era is harder to nail down) had a "wink-wink, nudge-nudge" relationship with the viewer. It got to the point where they had to acknowledge the equal rights movement, and at least pay lip service to gender equality, but deep down we knew, and they knew, that part of the Bond formula includes pretty girls, and the rest was just yakkety-yak. The scientist and the astronaut and the superspy would all end up in bed with Bond at the end, so let them prattle on about equality, so long as they looked good doing it.
Understand, I'm not a feminist and I have no problem with the above, because Bond is fantasy and for my money doesn't owe the viewer anything more than entertainment. And I really do think that women, as much as men, enjoyed the classic formula and were quite okay with settling for the merest nod to gender equality before getting back to the fun.
I don't think there really is much difference between Bond girls throughout the era's - which makes me question whether the films are depicting reality or have the Bond films (and all other films) help shape this reality?
I don't think Bond films reflect reality in any way, shape or form, and frankly every time they pretend to they lose their way. Bond is better than reality; it's fantasy.
But maybe your point is that popular entertainment helps shape the way we look at ourselves and the world around us, or maybe more accurately, how we choose to perceive reality and warp it into something we like better. In that case, I would agree the Bond series was a factor, along with the Playboy Club, sexy stewardesses, cigarette ads and a million other things that helped shape a fantasy view of sex and society in the 60s and 70s that women were asked (and may or may not have agreed) to play into. I think you could argue that as time went on, a certain segment looked back at the 60s as "the good old days" and because of it the Bond films continued to celebrate a 60s' view of sexual relations long after it reflected anything close to reality.
Even though Jinx's character didn't need Bond and her character existing in the 2000's (relatively new-age Bond girl) she was still subjected heavily to 'the male gaze'. We are forced to look at Jinx through Bond's own gaze when he picks up the binoculars and watches her exit the sea - we are forced to objectify her from a voyeuristic position. Jinx is coded to ensure her visual presence has maximum effect, so much so that when she exits the sea it is in slow motion - as if this is how Bond is seeing her in his mind.
She also ends up needing to be rescued, just like all the others.
Jinx, I believe, crosses a certain line that makes her less appealing than other Bond girls. As I said above, I think part of the game is that we'll allow a certain amount of pretension in Bond's "equals" because we all know, deep down, that they're not really his equal and we're just humoring them. Because, you know, they're hot and all. But Jinx is just a little too smug about it, a little too much the equal, a little too self-assured. She is, in a nutshell, not that likable. In that context, that lingering gaze as she walks from the surf seems in retrospect almost mean-spirited, like a pouty grumble that, "Yeah, well at the end of the day, she's still just a chick."
Also it should be noted that as soon as she starts talking to Bond, she launches into double-entendres as crude and witless as Bond's own, and it's not attractive (to me, anyway). I also didn't like it when Samantha Bond's Moneypenny was vulgar. This might be an interesting sidebar for your studies, too: that the Bond girls are expected to put up with, or even dig, Bond's childish innuendo, but if they ever engage in it themselves they lose much of their appeal. That probably says something about gender roles, but again that's not my field.
In fact, thinking about it now Bond is used by Vesper and the story is spurred on by her own actions not entirely Bonds. She is the first and original Bond girl - therefore can cinema be blamed for supplying us with these views of Bond girls as we didn't see a true representation of Vesper until about 50 years into the franchise, or was the cinema simply following/representing the reality we live in at the time?
Honestly, I don't think they put a lot of thought into it. To return to the comparison to cars, clothes and gadgets, sometimes we got winners, sometimes not so much. Certain elements of the formula were constant, but their effectiveness tended to vary greatly.