AVDD and Vref are from the same source, but it is ok because it is a low noise voltage reference source, and the only other device connected to it will not inject any noise.
If the problem of having them at the same voltage level is just with headroom, then we are happy with that, it will not affect our application as we won't be taking the input to the rail. If it will cause other problems then we would like to understand what they are.
Thank you for your help so far.
Best regards Martin