the moments you are supposed to feel unconfortable done even constitute 5% of the echii scenes and shots in the show. Sadly just because the show has good themes and you like it it doesnt mean that most of the echii in the show isnt straight faced most of the time or that most of it has "more depth and intent" than the echii stuff the exact same creators have done through their career. Imaishi who has used rape and sexual assault jokes all over his work, even in shows 1 year removed from klk, and has in mulpliple shows wrote eps where an underage character loses her panties and wears none for most of the episode wasnt thinking about commentary on sexualizing and its themes on the story every time he storyboarded and design boobs and asses all over the place (like 100 per ep). He just likes drawing sexy girls as he has actualy said in interviews

Most of the show being fanservice and being intended as fanservice of course doesn't have to mean 'the entire scenes only exist for fanservice' .You can get across themes while drawing something in a fanservicey way because you like booba and you target an audience that likes booba ( and not just men , klk had a very big popularity among many women who enjoy the "male gaze" outfits in KLK & draw very sexual yuri fan art of it) . There’s deeper story segments and symbolism that’s very empowering to women across the show but a lot of the sexual presentation and shots just exist as some inclusive erotica momments that both staff and trigger fans were into. Kill la Kill and director commentaries on the BD boxes also have imaishi and other members talking about "oh thats such a hot shot haha i had fun making this or writting this echii scene". The writer himself has called some of the bath and "supposed to be uncomfortable" scenes on the later part of the show "ship bait"

In general a lot of the takes in western fandoms aroud Trigger or Gainax or other anime stuff being deconstructions and commentaries and meta or having progressive social politics all over is often misunderstandings and lack of context of the industry's and creator's history and what they were or are fanboys off and instead projecting stuff. Here i'm saying thatImaishi & Nakashima come from a different both media and general culture-era background and focusing on modern feminism viewpoints and analysis to their stuff will have you attributing a lot of stuff there but which are present for much more basic and problematic reasons. BNA & Promare will go "racism is bad" but that's a normie take. Even the most progressive and feminist animanga authors or other japanese creators like nagata kabi & megumi igarashi would retweet stuff that says "if you have misandrist feelings you cant be a feminist". Igarashi would straight up argue with people she saw making "men bad" feminist takes. We have to adjust our lenses and expectations without stoping critiquing them

Back to Kill la Kill. Even in the meant to be uncomfortable mother-daughter scenes there still is an element of straight faced fanservice and creators going "booba". Trigger has sold art of that scene in official stores. Producer and /or director has said "it would be so hot if they made out here". And you can contrast with other anime. I find A Woman Called Fujiko Mine it's pretentious dreck but the way it did child abuse/rape scenes was very fucking different from how Kill la Kill did it (in a series that did have genuine fanservice too) is a good example of why lets say even the "its supposed to make you uncofmortable" ragyo bath scene also is supposed to be hot and be enjoyed at face value.Or utena. You don't have to draw those obvious "audience and camera focus on the sexy parts" shots, you don't have to give it an erotic color scheme, you don't have to use fleshy hentai animation and sensual music, you can get the idea across with something minimalist. aesthetic choices have meaning too

Show is self aware yeah but not "a critique or meta commentary or written as feminist" .It's basically saying stupid porny outfits can be badass, though that is not the core point, that's simply a part of the "giving personal meaning to aesthetics" theme. People see self-aware jokes or achii & assume the point is "this is bad" when in reality it's just that, a self aware joke made by creators that unironicaly enjoy those tropes and fanservice with a straight face. KLK's particularly porny for a mainstream work but it def has a higher artistic pedigree than that and has some good themes otherwise so people that like it are often met with the question of "wait, why is this doing the EXACT thing it's supposed to be satirizing or rejecting ?" and instead of realizing "maybe it was never that to begin with and and its just from people to people that love that shit" they decide it's some 4d commentary and deconstruction

I can see the point of the narrative, but I kinda agree with @geikei that, at least in the first few episodes, the fanservice seems to be a little more unironically sexualized. Where later in the more 'comfy' episodes, the art style de-emphasizes nude figures while still depicting partial nudity. IMO, they did this to hook otakus and weebs since that demographic brings in the cash. If the artists/writers were women, they could have gotten the visual message across more unambiguously (since weebs aren't often empathetic to the stuff you listed as being uncomfy) at the beginning, but Shoujo/Josei just doesn't sell well unless you corner a niche market.

I mean, that wasn't the worst bit in Higurashi. At least that had a clear purpose, even if it was super creepy. The real issue was everything with Irie and how he stays a 'haha quirky pedophile' the whole game even though it's made super clear just how awful the abuse Satoko deals with is and has the super effective bit on sexual assault. And then the story ends without ever doing anything about this fucking creep