It's important not to confuse the HTC Desire with the Nexus One here. The hardware platforms are the same but the software from the one is controlled by HTC and the other one is controlled by Google. The Nexus One has an open bootloader, the HTC Desire doesn't. All HTC phones released in South Africa so far have had locked bootloaders – the only way to exploit them was to use a kernel bug which gave root access and therefore rights to alter the internal flash.
So the HTC Desire *does* have a locked bootloader, the only advantage it does have though is there are have been so many HTC Android predecessors that there are various bootloader options and hacking methods (goldcard, etc). The Milestone has a fairly new release and the same wealth of information isn't available. It is being worked on though, hopefully they'll crack it soon.
On the brighter side though, my Milestone is now running Android 2.1. 2.1 capable devices sold locally like the Hero and Magic are still running 1.6. HTC in a way force you to crack your phone, while Motorola have so far tried to keep up. I haven't felt the need to even look at cracking it.
Both the HTC Desire / Nexus one and Milestone are great phones. It's really difficult to choose between them, I think it really shows how the platform is maturing and any new, reasonably powerful Android phone would be a good choice