Bottles has certain sandboxing capabilities on top of wine. Plus, Bottles can download and manage various wine versions, separate from your distro's offerrings. It's pretty neat. Of course, technically, you could do almost everything it offers manually via scripting and your own wrappers, but that can be said about almost any software. Heck, C and C compilers are nothing else than syntax sugar for writing assembly.
To expand on this, at least historically, Wine unfortunately didn't progress in a straight line, often new versions came with additional features or bug fixes which made some applications run or run better, while others ran worse.