It basically goes back to versatility vs convenience. I agree that all other things equal, an extra USB-C port will always be more versatile than a HDMI port, because you can transform the former in any port (or combination of ports) you want with the right adaptor.
The benefit of a dedicated HDMI port would basically be that you don't need to bring an adaptor with you to meetings (and even then, only if you are slated to give a presentation). Because back at your desk, you will likely be using a dock to consolidate all your accessories and connect it to your laptop via the USB-C port either way (which incidentally, also means that you won't be using MagSafe).
3 Thunderbolt ports is likely still plenty for most users. If you didn't need all 4, you would be indifferent between one being converted to a HDMI port, I suppose. We will see if this is something the pros really do want, and not just a vocal minority (who were never in the market for a MBP). I do hope it's the former.