As I already told you, I am not an expert in web development. Downloading 1000 files or just 1, if they weigh the same, it should have the same download value.
But I do understand that 1000 files consume more IO than just one.
Normally we do not worry about IO or IOPS in webhosting, but if you have a server with hundreds of thousands of games, possibly it is something to take into account (For some reason, web hosting places a limit on these values), for That's what I made my comment to you.
I don't know if this is the reason or not, I don't work at Itch, I'm just pointing out that if there is a difference and that maybe it's a reason why Itch placed a limit on the number of files, I'm not claiming that that is the reason.
If you want to know the real reason, the only one who could explain that to you is the admin, all the rest are just speculations.