Keyboard shortcut aside, every other thing (design and functionality) remains the same. Only users of the WhatsApp Desktop app will be able to utilize WhatsApp keyboard shortcuts to change message read status, mute chats, move between chats, and lot more. For the latter, keyboard shortcuts are limited and not supported. In terms of functionality, WhatsApp Desktop trumps WhatsApp Web. Design-wise, the WhatsApp Web offers the same aesthetics as WhatsApp Desktop. On both interfaces, buttons, tools, and icons are arranged similarly.
Both the WhatsApp Web and WhatsApp Desktop are designed similarly such that they both have (almost) the same design, features, and messaging experience.