Games on Itch are usually not "installable", they are unzip and run.
Commendable that you do use the html5 features for loading on demand. This is why I a voice my bafflement about the restriction. This is not the only thread about this topic.
I have yet to see a good explanation why the number of files indicates a lazy export from a game engine that results in a bad user experience.
Because as I understand it, you did not export this and had a lot of files because of that, but you developed for web directly. Making this explanation "many files = lazy engine export" be rather questionable.
Would not an engine developer quickly learn about such restrictions and have an option to reduce file number, but otherwise be as lazy an export as before?
I would understand it, if it was said that number of files puts strain on the servers or any other explanation. But I do not follow the chain of logic that is currently used. Or that is used as far as I understood the explanations.
In one of those threads the developer tried to pack the files only to find out that the packing method used could not be used over web, because the unpacking method is not allowed for security reasons and only works on a development build on local client. Did not sound like a lazy engine export either.
I do understand the discouragement of lazy engine exports that would work better as a download version. But I question the method of using a file counter as an indicator for this.