You're right, and what you pointed out is indeed strange. I see two explanations for that: Either those girls aren't actually pregnant princesses but members of the "society" that didn't go through the process because they had other roles or they are pregnant princesses who realized this possible issue and sought out special futanari seeds (likely using futanari fairies' whatevers) to avoid impregnating other pregnant princesses.
Well looking again the hot spring gangbang really have to be other pregnant princesses, as to even enter the hotsprings you have to be one, the person at the front desk litterally say "Since these hot springs are for Princess use only, your monster allies must remain in the resting room to the right.", and when in the actual bath there are multiple things that clearly tell that it is other customer of the hotspring that is actually doing the gangbang, one example being one of the girls in the bath, that is litterally "named" "Beastwoman Pregnant Princess", saying "That was the first time I used a futanari seed, but it was nice. I've got to get as skilled at being a futanari as being a Pregnant Princess."
Also I don't think the futanari seeds have anything to do with the Futanari fairies per say though, but is rather just a normal seed in this world, as they do appear in both "Lily knight saga" and "Forget-me-not Gemini Fort".(Both taking place in the above world even). One other thing that could be argued could be that the princeses in the hotspring don't yet have the "natural" futanari abilty, that a pregnant princess can get, which At least Eliza gets at the time of getting the Tentacle suit, and Jard seem to have it as well when the 2 have their scene together, probably gotten while in captivity of the fairies before you arrive there. But if that is the reason she don't get pregnant there, that does leave hanon as the scene with Hanon and Eliza is clearly with a Futanari seed, which means that Hanon at that point, don't yet have the futanari ability either (if she ever gets it, there really is no indication at any point she got it, but that could just be a matter of there not being a need for it to be shown to Eliza over the course of the story ofc), which then would mean that the impregnation between them there in the grotto before, should not be able to happen either, so yeah at the end I think there is some sort of plothole here, no matter how you twist and turn it sadly
Thank you for taking my question seriously, by the way.
You are welcome, I freaking LOVE this game, played through it 3 times, and at this point have been doing a bit of a mod for it as well (managed to grab the RPGM VX Ace engine at a very heavy discount, to be able to do it, man its not worth the full price this engine though), so this discussion could potentially give me some idea for that maybe even
I am not making any promise
when or even if I ever get the mod finished though (thought initially this was something quick I could do in like a week or so, back in I think it was october or november, well guess what I am not done yet

, things often are not as easy to change as they seem on the surface for games

), but essentially I am allowing multiple degrees of pregnancy, by allowing multiple impregnation at once (up to 5 times, with different belly size representation to match it), and then allow mixing and matching of the monsters equipment at birth-time with the different monsters that you are impregnated with. Probably also gonna look at giving some of Jupiri's powers over to Gospel instead, as lets face it, Jupiri is just WAY OP compared to any other monster, and anything Gospel can do when you get her back in the HQ, Jupiri can do better, and much more anyway, as well as making Gospel able to get trimmed as well, as she does perfectly fit the criteria laid out for it by the game as well. Though before I touch those part I want to be done with the pregnanacy/customization parts first