No, its not a programming problem, its a herding problem. That person will have to have the ability to get all 3 implementations to agree to read and write compositing configuration the same way, so users don't have to suffer.

The thing is, Wayland actually is an improvement here, because now you only have to reconcile the configuration between those implementations, compared to before where you had to do that in addition to munging configuration and state stored in the X server and in xorg.conf. It would be nice if all desktops agreed on a configuration format and a default set of options, but I don't know that we will ever get there.

At least between-app DPI inconsistency was not a thing before this. Now its a thing, added to the stack of configuration problems.

If you support multiple DPIs then that will always be an issue, regardless of what display server you're using.

Not if the protocol allows the exchange of desired DPI/scaling.