Just as a note to the overall feature request, this is unlikely to ever be added for one simple reason: with one very small exception, Layouts have nothing to do with projects.
They are a generalised tool for reproducing layouts across whatever projects you use. Quick Reference windows are intrinsically bound to one very specific binder item from one specific project. They are a window that exists for that singular purpose of displaying the content of that one item.
The other issue is that I primarily see this being suggested as a way of solving a bug: QR panel are not saving their position and settings persistently across session. Spending inordinate amounts of time solving a bug with a completely different system that has nothing to do with that bug is not the best way to fix bugs. We should just fix the bug, not potentially create a dozen more.
As for why they don’t save Copyholders, the main issue there is again a somewhat project-specific problem. If the copyholder is not built with specific UUID from your project window then it comes up what, blank? So now you’ve got to use a menu command, or drag an item from somewhere into the header bar to make this blank rectangle eating up part of your screen useful—and guess what, that’s exactly what you do to make a Copyholder in the first place.
So we’ve saved you nothing by stashing it in the layout and restoring it upon use, zero benefit to your efficiency, for the cost of providing something that always loads up awkward and empty (useless).
It’s an idea we’ve tossed around a bit in the past. The main issue with going in that direction is that it would pretty much mean having to commit to it fully. The notion of having a set of broadly useful layouts you use across all of your projects, past, present and future, would have to be abandoned for a system that forces you to recreate those setups in every project, every project template you create.
It wouldn’t be terrible, but when considering the benefits vs what is lost, it’s debatable as to which is clearly better. And if you’ve got a problem like that where there are a lot of pretty strong pros and cons, then overall radically changing a system to work another way is usually not the best path to take. For one thing, you’ve got a lot of silent people out there that are using layouts the way they are, and if we take that away from them and make it a project-only tool, they will no longer be silent about it.