Yes, likely a combination of different factors.
There is no system level function “minimize to tray” so if an application wants to have this kind of behavior its reaction to being minimized is actually closing the window.
That makes it disappear from any task manager, window list or similar UI.
I.e. as far as the system is concerned it doesn’t have any window at all.
Hence manually closing the window resulting in the same behavior.
This most likely fails with Wayland because windows are usually not informed about their window being minimized.
Compositors can consider this an internal state and handle it in any way they see fit.
If system with taskbar might just hide the window and change the state of the taskbar entry, a system without could “roll it up” into the window decoration, or reduce it to a thumbnail or dock it somewhere.
I guess it could be framed as such.
While client isolation is one of the design choices, it is more a bonus of having a new system rather than a reason.
Theoretically one could also introduce client isolation on X11 but most clients wouldn’t be able to cope with that.
Also, the approach of confinement is, and has been, widely used in other aspects of the operating system.
For example user’s can’t see, read or write each others’ files, they’ll need a shared location and respective access rights to do that.
Wayland just extends that to windows and by default.
X11Libre’s xnamespaces can do the same, just not enabled by default as many X11 clients expect free-for-all.
I would be surprised if the majority of users copy from or paste into a non-active window.
In every other aspect the two systems (X11 and Wayland) handle copy&paste (and drag&drop) in a very similar fashion, a data exchange between a source and destination window.
Not really surprising given that there is a large overlap in developers working on them 
As @stlnb pointed out the only real difference is that on X11 any window can overwrite the current offer at any time and retrieve a posted on also at any time, while Wayland essentialy only allows either operation only for the window the user is currently interacting with.