I'm not a web expert, nor do I work for itch, but I understand that the file limitation has to do with the cost of the server.
It is more expensive for the server to provide 1000 small files than a single large one.
Remember that when you run a web game, you do not download a zip in memory, otherwise you request individual files.
Therefore, the games that are downloaded do not have a file limit.
Surely you are going to tell me that 1000 or 2000 doesn't make much difference and you are right, on a small scale. But Itch is a company that is close to having almost a million games on its servers, for them, the volume of passing the limit to 2000 surely means a significant increase in the cost of the servers.
Edit: In your case it may happen that you have 2000 files and that each file is a page of a book, but there are people who will have 2000 files on the same level of a game. The problem with this type of limits is that in one case they do not make sense, but in other cases, they do and many times you must cut somewhere in between.