How can I optimize storage for multiple similar folders?

For your project, creating custom Prefix folders can be a good approach. Typically, you only need two: one for Win32 apps and one for Win64 apps. This way, you can prepare them using winecfg before installing any applications. It’s also easier to automate the deletion of apps and provide sandbox capabilities, which seems important for your goals.

You might want to look into using btrfs subvolumes. They can help manage disk usage effectively by allowing you to create copies of directories that only save differences, rather than duplicating everything. Make sure to check out the `cp --reflink=always` command—it’s a handy solution, although it is specific to btrfs.

If you're using Steam, it automatically handles this via symlinks for different Proton versions. But if you're looking for something that works independently, you might consider an application like Bottles. It's not perfect, but for most users, it can help manage Prefix folders efficiently and minimize space usage.