The main clash I feel here in theme is the fact that biomodding is a product offered by a megacorporation and advertised as such. Style over substance is a core part of cyberpunk, yes, and I agree that ICly we represent this with biomods having PDS costs: the catboy solo doesn't get to be as effective as the non-biomodded solo. That to me is theme; because cyberpunk isn't about style with no cost.
Style over substance is meant to represent how powerless people carve out something of their own within a system that wants to homogenize and commodify everything. A major part of cyberpunk is erasure of identity and self-expression due to consumerism. It's a world that's hostile to your body, and your choices.
When a character gets biomods, to me, it's not meant to just be a cosmetic quirk. It's meant to represent giving the middle finger to your oppressors - choosing to be yourself and express yourself in exchange for losing your edge in a system designed to optimize efficiency and human resources. It's the purest expression of cyberpunk defiance and resistance. You give up survivability in the name of self-expression. Take a solo who is biomodded versus a solo with the IC/OOC 'meta' of the standard typical solo chrome suite. The solo who's expressing themselves and refuses to conform to what society thinks is optimal is far more cyberpunk than the other.
The world punishes you for not optimizing, for being too loud, for being too weird, for being too you. It's a commentary on how the modern world does the same with marginalized people: too queer, too different, too weird etc. It's what the current modern society does to people who are trans, neurodivergent, disabled, or anyone really who steps outside the cisnormative, technocapitalist idea of 'useful flesh'.
That's what style over substance means - when the expression of self is more important to you than your edge, because it really might be the only thing you can own that's actually yours in a cyberpunk dystopia. Even if it gets you killed… especially if it gets you killed.
Not punishing stylistic choices would take away the theme of that for me. It costs everything to be yourself under capital, and that's what makes it worth something. If there's no cost to style, it becomes a fantasy. However on the other hand if there's only cost to style, then it becomes oppression.
This is where the theme clashes a little bit IMO. The game punishes people for expressing themselves with chy and PDS costs, as well as thematic groups such as NOMOD. That's fine. However, there isn't much of a benefit to off-set those drawbacks both mechanically and IC.
Biomodding is a commodity offered by a corporation which means your self-expression that's meant to be a fuck you to the system also kind of contributes to the system. That's fine: that's cyberpunk to the extreme. It makes the narrative even more tragic: even your desire to be yourself is something that the corps profit from.
The clash is when it's also advertised as something that corporate elites do. This is also much of an IRL thing: example tattoos and piercings. A poor person with ink and piercings may be seen as a criminal, or filthy, whereas a rich people will be seen as edgy, hipster and so on. Yet IMO it still leads to a clash where the punk is taken out of the biomod angle and is 99% of the time treated as a corpo thing.
If it were me, the solution would have to be layered:
a) differentiate between corp and mixer biomods. Corporate aesthetics/trends are different than the Mix. Maybe corp biomods favor clean, symmetrical, aesthetic mods while mixers prefer loud, grotesque, attention-seeking, shocking, animalistic mods. While corporate PCs and NPCs might see biomods as 'elite', anything that's non-conforming, shocking or against topside culture should be ICly seen as awkward and weird... whereas the Mix should embrace the individuality, no matter how fucked up it might be.
maybe even have it so that the biomods sold to the Mix are of second tier quality, or even have black market biomods so there's an IC justification for how Mixers are eating the crumbs of the top shelf mods that corpies have access to (without any mechanical repercussions, just that you have to go to CWH if you want clean/corporate looking mods whereas more gutter looking mods are done in CGH etc.)
b) give a rather significant CHA boost for biomodded people if their mods are visible and maybe even change the CHARM substat to not be how -likeable- you are, but how -noticeable- you are. Because biomodded people should be turning heads and have more presence regardless of wherever they are, because they are -different-.
c) allow some chrome to be opted in as biomods instead. this is probably going to have a lot of pushback, but if someone wants to have cat ears instead of an amplifier chip + cyberear, handwave it ICly as a partnership between SK and VS or something and let people have cyberears in the form of standardized biomod packages that give you ears. unnatural eyes? cat eyes? cybereye + lowlites. equalize the PDS costs so they're practically the same as if you had the chrome installed.
d) introduce narrative plots aside from NOMOD that prioritize modded characters in a POSITIVE light. have a biomodded punk subculture in the Mix: maybe have a club where splicers hang out in often, like IRL queer spaces, and where Mixers -accept- people who are outcasts, 'freaks', anarchists, whatever.
introduce a faction of anarchist biomodders that reject the corporate ideal and try to biomod their body to the extremes to push the limit of what can be done, just to shock topsiders and mess with corpies, or believe the body is a canvas much like IRL extreme bodymod fanatics. reverse the narrative where while NOMOD might call people freaks, this subculture adores it -- and being a 'normie' makes you a loser.
Anyway, I've written long already but those are my few suggestions and understanding of theme. Hopefully it helps the discussion.