TL;DR I think no for top (and middle?) women but yes for bottom women.
Part I: For the top women:
Wait a minute...'top woman player needs to be able to finish 2nd or higher in the open category, or she might as well play in the woman's section' - I believe the point of playing in any tournament regardless of your gender is that you're indeed aiming for at least top maybe 30%. Since the top women cannot do this, women's tournaments are created. I think there's something mixed up here...
It's not that we have 2 tournaments and then there's this kind of an incentive problem. Rather there's a sexism problem and then the 2 tournaments help make up for this sexism problem. I don't think there's a need to incentivise women who are already professional women's chess players (like at least 15yo already) to enter open instead of women's.
But I do think there is a different kind of 'incentive' problem, namely the is the sexism problem: Because of sexism, women who aren't yet professional players eg 6yo girls don't have much incentive to study chess at the same level as boys of similar age (or rating?) and thus later on they're not able to compete for the open tournaments.
So I think the issue with your question is that you're focused more on the present generation, rather than the future generation, of female players.
Re what Mobeus Zoom said
Now I am wondering whether Polgar's lifetime prize money surpasses Koneru Humpy's for instance
Actually I think Hou Yifan - if it weren't of course for that Yifan retired kinda early - is a better example.
I'm not so familiar Judit's career, so I'm arguing a priori not a posteriori:
I believe it would be nonsensical for Judit to stubbornly compete in open tournaments whereas Judit could do better in women's. My guess is that Judit was just that damn good not just as a female chess player but as a chess player (well, Judit not only beat Susan's record of youngest female grandmaster but also beat Bobby Fischer's record of youngest grandmaster) s.t. on average Judit gets at least the open equivalent of top 1 women's.
In your example top 1 women's is 25,000 which is the same prize as 3rd place open. So if Judit has the choice of competing in 2 such tournaments and chooses open, then Judit is winning on average at least 3rd place.
However, I have a feeling Mobeus Zoom is on to something. After all, if Judit gets (I'm just gonna present tense to talk as if Judit is still an active player and nowhere near retirement as part of this answer's being an a priori answer) 3rd place on average then Judit is getting regularly placed 4th, 5th and maybe even the occasional 10th whereas Judit is sure to get 1st place almost every time in women's tournaments.
Maybe for this part it isn't all about the money for Judit or at least for the short run. I suspect any (combination) of the following:
A - Judit might be talking slightly lower pay (I don't imagine it's much lower!), but Judit really enjoys playing against stronger opponents.
B - It's an investment. Judit might be taking a hit in the short run but is expecting to become a stronger player and thus indeed get 1st and 2nd place prizes s.t. it's more profitable in the long run to play open tournaments.
C - Judit earns more overall by playing in open tournaments not from the tournament prize money but by making money through having more credibility to be a coach or chessbase instructor or guest on a podcast or something. This credibility might even increase from future awards like Judit might be inducted into the World Chess Hall of Fame someday and thus have even better post-retirement from professional play employment prospects.
But of course emphasis on 'slightly': Money is indeed a consideration, so the above really assumes you can regularly compete for top 3 and stuff. So it's about money but not all about money.
Btw, in case you're suggesting in the case of 2 tournaments that we should set 12th place open prize = 1st place women's prize (and then adjust accordingly 1st to 11th), I see a problem assuming exactly 12 players per tournament: Aleksandra might play open but then will you do as you say 'sign up for the open section, lose every game, and pocket' the 12th place open prize.
Part II: For the bottom women:
Yeah I guess you're right if we're talking exactly 12 players each, but I think it's an easy fix.
Conversely, the weakest female players should play in the open category, since even though they will probably get pulverized they're still likely to earn more than in the women's category (I imagine however the organizers will forbid this).
1stly, I don't think players who would be bottom players of a women's tournament would be invited to an open tournament if, say, the tournaments bottom players dropped out because there are likely many other male players on the tournament's waitlist. (Probably female players are on the waitlist too, but they don't much monetary incentive to play open as discussed above.)
But I believe it's fixed if the lower 2-3 prizes in both open & women's are the same.