OK, I wasn’t going to comment any further, but this is a great point. If that’s too much of a technical barrier for anybody, maybe they should not be contributing to a manual of complex 3d software like Blender. I think that’s a great quality control feature. Now that’s it. 
That would be best, as there’s only so much of your passive aggressive insults I can manage before you’re going to see some personal attacks and moderation.
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Wow, I was going to ignore the condescending tone with which you reply to anyone having a complaint about Blender but this is incredibly stupid, really.
Why would I blame myself because a functionality or feature has bad UX and it’s unituitive to use? Your answers make no sense sometimes
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I’ll save Martin some time:
“It’s only unintuitive to you, because you’re too stupid to use complex software.”
No, Thorn. Not only I never said anything like that, but I actually never think like that. We are simply talking about software features here. I never ever think that knowledge about some specialized software has anything to do with being smart or stupid. Most people I know in my life know nothing about Blender or most software I know tons about actually and the thought that this has anything to do with how smart or stupid someone is makes absolutely no sense to me. I just don’t think this way. So if I ever say that the problem is lack of knowledge I never mean that to be an insult. I would be insulting myself as well because I lack knowledge in many things myself - that’s normal. I think it is useful to adapt to how things work and find a way to atchieve your goals with tools available.
In this case, Blender has hotkeys for adding objects to collections( Shift + M ), moving objects to collections( M ) and also adding objects to collections that do not get linked to the scene( Ctrl + G ). So anybody can choose what they want to do with this. That’s it. And I don’t want to offend anybody with this information, that’s just how it is. Now if you choose to be offended, I am sorry to hear that, but it was not my intention to offend and as far as I understand it was reasonable for me to expect no one would get offended. Now stop painting me as the bad guy here just because I express my opinion and also try to share my knowledge - I am certainly not attacking anyone personally and not even talking about anyone personalty.
It’s confusing, but most of the software maintains its previous version of functionality. I think that’s the case with this. 
The link is where you can see more information about Ctrl+G.
What I tried to communicate, is that there will always have unlinked collections to scene ; at the moment, that you are dealing with a blend file containing 2 different scenes.
The purpose is to hide it from the View Layer. So, the info can’t be in the View Layer display mode as a collection of its collection set.
If you are not aware of those collections and don’t use them, they have no impact on your scene.
But you are right. If you know about them and use them ; although those collections are not valid for a View Layer, they are undoubtedly used into the scene.
But we are not completely without any indication.
We just have to switch to Blend File > View and Collection filter to immediately see them present with a fake user. That is an easy check.
We can see their content. We see what objects are in it.
When we know the objects, we can deduce in what scene they are used.
So, if you suspect that you have scenes with a weird behaviour because of them, you can track them and debug scene.
If you are fearing to have created unnecessary data, by using shortcut by mistake, they will be displayed in Unused Data view.
So, you can clean your blend file and deactivate the shortcut.
There is no reason to consider View Layer display mode, as alpha and omega of info about your file. There is no reason to complain, that a change of mode is necessary to have an info. User can create a workspace, containing multiple Outliners in different View modes.
But if an unlinked collection has a user in scene, there should probably be an icon next to modifier using it.
Ideally, existence of a Rigid Body World should be mentioned, at least in Scene view. Same for existence of an Effector Collection for old physics, too.
But that would be work for a workflow destined to be replaced by GN, for a feature mostly ignored by users.
On the contrary, use of a Collection Info node in GN in a nodetree could display same info as a Boolean or Line Art modifier in Outliner.
The users of those collections will continue to be modifiers.
Looks like I didn’t made myself clear… Again, I’m aware of all the things you just explained. I get it, my default scene even has two outliners, one in viewlayer mode and the other in blender file mode.
What I’m trying to say since the beginning is that still the use of Ctrl+G to create hidden collections is clunky, the UX is poor and it’s only obvious/easy/clear to those who already know about the feature. It should be clearer, both from a UX and UI perspective.
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The initial intention of developers was to remove the shortcut. Like what is supposed to use it was intended to be replace.
We asked to keep it, because they did not provide a replacement and did not think about one.
Seriously, that is not our only and worst UX issue. Other things should have priority over that.
The thread, about welcoming Modo users, reminded me, that Outliner does not really allow other operations than selection, for multiple objects.