Same with a guitar. There’s no complaining that an SE has “S” pick ups, veneered/laminate top versus solid pieces on the Core, a cheaper, plastic nut, cheaper, imported electronics, etc but if, in the example of my experience, there are globs of glue on the sides of the frets, peeling top coat/paint along the side of the frets
I would argue that the issues you mention here are not 'just' cosmetic but affect the feel and playability. The neck is an area where a players hand is going to be, running up and down the neck and so should be perfect, no bumps from globs of glue or peeling finish. That is vastly different from say a bit of dust under the finish that cannot be felt - even if its on the neck. The 'finish' still has to be 'perfect' in that its not peeling away, lifting or not smooth after sanding and buffing.
The point I was making is that something that is 'purely' cosmetic only, doesn't affect the guitars feel, playability, tone, functionality (finish can be argued that it protects the woods so would still count as an issue that affects the 'function' of the guitar - especially on the neck for obvious reasons as that affects 'feel' too), etc is subjective from person to person and not enough in my opinion to scrap a $1k guitar over or spend a 100hrs+ trying to remedy.
The offset birds, not perfectly centred in the fret, does not affect the playability, feel etc in any way, they also still indicate the correct frets, they are not half way between to frets for example and confusing as to which fret they are supposed to be indicating. Its not worth ripping the fretboard off and redoing a new fretboard, new frets, new nut, refinishing etc for a few mm's of difference that doesn't impact on the guitar, its feel, its function (inc the fret marking of the birds as they are still marking the correct frets), its playability etc. That would be completely different however if the birds are positioned correctly but the frets are what's positioned incorrectly as that affects the function.
Complaining that a 'back plate' has a small gap at one end, something slightly wider than the rest of a recessed backplate for example has absolutely no impact on the guitars function, playability etc either. Its still doing the job of covering the electronics, not causing any 'buzz' or rattle from being loose ,or not protecting the electronics from dust.
If you want to use your metaphoric car, the one that has clear coat is peeling and there are giant weld globs and the logo on the hood was put on upside down, the clear coat and weld globs affect the function of the finish, which is to protect the cars bodywork. The weld globs may affect things structurally as well as be prone to rust if they are not covered too. The 'roof sticker' though is just purely cosmetic and, if the finish was perfect and the sticker was under it, that's not a reason to complain. If you don't like it, don't buy it - someone else may think its 'quirky' that its different and like it. Its not affecting the car in any way at all, not affecting the car's 'finish' that may lead to rust and structural damage because the protective coating isn't 'perfect'.
Its like finding a PRS SE with a 'chevron' style flame maple veneer and wishing that the direction was angled the other way, that to you its 'upside down'. All the others may point a different way but that one is just 'different' and not a reason to complain. If you prefer the other ones, by those but someone will come along and find that one to be unique, different, quirky and as long as its fully functioning, still sounds, plays, feels etc like all the other SE's, buy it.
Anyway, I think I have stated what I think enough. I am certainly not saying that things like peeling finish or globs of glue on the frets are the same as some purely cosmetic issue as these not just purely cosmetic issues but have an impact. Therefore these things should be sorted before a guitar makes it out of the factory to retail.