Yep, it's a "feature" of the classic Amiga OS, and it's also possible that Wordworth is doing its own internal calculations in the same way, meaning that even a patch for the OS wouldn't solve the problem. Usually it's perfectly safe and harmless once the filesystem itself knows the correct size, but sometimes (like in this case) it causes issues.
Another alternative might be to create a hard disc file for WinUAE which is less than 2GB in size. You can install what you like there and keep it, or even install it and copy it over to wherever you like, and update the assigns etc. to suit.