In my opinion:
a) they choose a certain very specific ideal as a target, but utterly failed to convey that to a majority of site visitors;
b) their picked target and path visually and functionally matched by like 90% with a thing already existing for decades previously and very familiar to a majority of internet users - with a regular forum with sections and treads;
c) they make fundamental errors even inside the scope of their own ideal and vision - like for example apparently not taking into account that software with identical name can have different versions;
d) while they copied forum structure (failure B) they also failed to envision (or did a mistake in that) how the ideal target result would look like a long time in the future;
e) they failed to acknowledge all of the above, reflect on and fix own mistakes, instead they declared those mistakes "a culture" and persisted in deepening them;
Basically they picked a forum format, known at those times to literally everybody on the internet and decided to use it to make something vastly different, while failing both at communicating that intention and also failing at actually adapting UI and tools to better suit their target.
Very well put. Except they didn't think they were "picking a forum format". Forums with that style of voting were still kinda rare at the time (Reddit was young at SO's date of creation) and the Q&A formatting was supposed to look intentionally different from a "thread", which is also way (at least in the original design) comments were de-emphasized, and moderation policy held that the large majority of comments could be deleted at any time.
Unfortunately, this design comes across to a lot of people as comments being threaded replies, and the "question" format as privileging the OP (which makes it that much worse when the system forces question closure to happen out in the open). And recent redesigns, by new ownership obsessed with "engagement" and profitability and apparent complete apathy towards the original goals, have thoroughly enshittified the original.
I also have no idea what you mean about
> for example apparently not taking into account that software with identical name can have different versions;
There were always separate tags for various minor versions of Python, for example, and they were commonly incorrectly applied to questions where the version was not relevant.