The verdict
If your customers already live in WhatsApp and you are a small team answering a few chats, start with the WhatsApp Business app. It fixes the basics, such as a business profile and automated greetings. When volume grows and chats need an owner, routing and a hand-over between colleagues, put a helpdesk behind it. If you are sending requests through email, forms and phone and need structure, pick Freshdesk.
For most small B2B teams the helpdesk is the stronger first choice, because it works whatever channel customers use. Add WhatsApp when your market expects it. Keep your core customer data in your own systems, because Meta sets the message rules.