Actually... Wayland fully supports transparent windows assuming you have a buffer with alpha transparency, and windows have no decoration by default. It would take a very small protocol extension to allow overlay windows which don't accept input of their own, allowing for Redshift (and other tinting tools, such as those for dyslexia) to implement such an extension without embedding it into a compositor.
Wayland has a process for standardising extensions - write the XML file defining it and send an email to the mailing list, then respond to questions - if developers cared about Wayland, they could do it.