That is sadly part of a fear that many people will have. People reading the itch version will always second guess everything. When one scene ends, was the scene experienced in its entirety or was some dialogue and images removed? They will have to wonder, was a sentence taken out or was an entire paragraph taken out? Did we see all of the cuteness from Marruk or were we deprived of some of the cuteness? While it was made clear from other replies that the story is going to be told the way it was always going to be told, that can still be an area of nuance. For example, an anime that does a faithful retelling of the story from the manga, will often have a lot of content cut out compared to the manga. While you will still get an understanding of the story, if you go back and read the manga, you will still often find dialogue that reveal little things about a character that while not very important to the plot, it works to add more substance to a character. Other times it can be smaller details that contribute to world building where the anime may skim over in order to maintain pacing to have a strong showing for the first 12 episodes.
One of the issues that has lead to such widespread overreaction (itch initially delisting all NSFW including simple strong language and violence), is because the responses from Stripe used terms that are subjective in nature. There is no telling if their definition of adult content was narrowly defined as what was seen in in the game mentioned be collective shout (a game which both platforms quickly removed long before the censorship campaign ever started), or if they defined it more broadly where anything more extreme than Mario Cart is considered prohibited.
While my example is more extreme to convey the concept, since there are many ways to interpret the verbiage, it will be impossible to understand how far the content filtering/ censorship goes, and due to how VNs often work, it can be difficult know what is missing, and that will create a sense that something is missing with many scenes, even if nothing is actually missing between the censored version and the uncensored version.
One potential workarounds will be to clearly indicate when something is censored, but that will then interrupt the flow of the story and change the overall experience. Imagine watching a serious movie and in a scene, the actor pauses a conversation they are having, and looks at the camera and then states that on the 29mm T 1.8 lens on the ALEXA mini LF is not fully centered of the focus ring and that will lead to uneven wear on both the focus ring and follow focus module. Something like that will change the whole vibe and feeling of the movie.
Overall it complicates things in ways that seem unnecessary considering that other VNs, including ones with lots of NSFW content are back to posting uncensored updates with no negative impact to their listing.