This has been hashed over many times. It's not just Android, it's pretty much all flavors of unix and windows as well. Even iOS has limitations on how much free space you need to operate efficiently. In the old mainframe world (yes, I lived it, lol) it was the same, but do you know how much memory IBM mainframes had in the mid 80's? 64K. Yes, K. Just like the original IBM PC. But they had such fast I/O and were swapping things in and out so quickly it seemed like much more. You could up the memory from 64K to 640K, but the price of a mainframe went from $2mil to triple that.
All OS's will always be limited by the need for space to work, unless you give them so much real memory it wouldn't matter. But the cost would skyrocket. Faster disks help, for example SSD drives with windows make it fly. If we had those instead of SD, then this issue would be greatly lessened.
Perhaps Google, and others, should count that requirement into the OS requirement and state out right 2.5GB for OS, or 3GB for OS. But it's a marketing thing, to make your storage seem like more that it is. Techies will know this, the common man won't. And most devices are aimed at the common man.
Now that you know, for the future, keep it in mind. Whether Android, Windows, Mac. Doesn't matter. The space you start with, the open space you see, the "usuable space" is not necessarily how much you can use.