Yes, other programs are a bit more forgiving in this regard as they tend to allow layering on top or even editing a 'copy' and where the users wants a linked copy they have to specifically designate that.
I tend to think that the other way around would work better myself but after looking into the matter have convinced myself that technically a copy is exactly the same (and remains the same) as the original whereas a clone is a copy that at the time of cloning is the same but then can grow and change into something else. As such I think OpenToonz techically gets it right but there will be an eternal line of new users that are accustomed to generic copy paste operations that don't link copies. And... in most cases we would not want those copies to be linked because we might inadvertently alter the original.... yikes.
A potential solution would be to allow a dialogue box to open by default upon a copy/paste operation that specifically informs the user of what is happening (linked copy versus cloned copy). An option would absolutely need to be there to turn off the dialogue because most users will most definitely not want it to appear each time they make a copy. But until it was turned off the user would be getting educated on the difference.
I tend to map Clone to an easy keyboard combo like Alt + C to stay near to paradigm of Ctrl + C for copy so the only difference in execution on my part is using the Control key or using the Alt key. If I recall correctly I had to borrow Alt + C from something else (the lipsync feature or something close to that). As I don't use whatever that shortcut key combo is often it made good sense to change it.
Added: The problem with the example you use is that neither appear to be exact LINKED copies that will always be the same. That's the important part of OpenToonz copies. Once made they will cascade update every time one of those copies is updated. Again, an instance (in 3D or otherwise) generally may be a linked copy but data can be layered over it in ways that override and change the copy. As far as I know there is nothing quite equivalent in OpenToonz outside of FX nodes in the Schematic that are applied to each instance of the copy. They can alter the data of the original but always do so in a non destructive manner where.
Perhaps a more appropriate term for a copy in OpenToonz than 'instance' might be a 'reference' because the 'copy' refers back to the original..
It's like an HTML reference that doesn't actually make a copy... it only references the original source document.
As such, working with linked copies/referenced resources operations are much faster because multiple copies of multiple copies of multiple copies don't have to be referenced.
Technically, in OpenToonz a (linked/referenced) copy is more desireable than a cloned (unlinked) 'copy'.
The terminology does get confusing! ;)