ioquake3 is an updated/improved quake 3. I’m not sure what you mean. There are other forks that are not compatible with regular Quake 3, we generally strive for compatibility.
What download links? If your talking about the Github page I posted, is the open source project, and like I said is based of an early ioq3 version. Is intended for more performance rather than all the extra ioq3 has gained over the years and as you can see is being actively devd even looking to include vulkan within its main source