After using it enough, i just can say about workflow having a game engine directly integrated in a full app like Blender is superior to most other 3D engine about workflow when you have changes to make.
You can test your game and at any time; and tweak or add anything while staying in Blender without having to switch between 3D engine and modeler or without having to deal with import export :
edit a model change UV texturing or materials use shader editor to change materials (other 3D engines also do) create new animations or tweak paint or sculpt and test directly change your level design add new models and layout and test any time without any import export
Another advantage is coding :
easy language game engine logic easy you can create any sort of plugin in the fly, to boost your workflow, very easy
Other engines can have advantages about tools to speed up workflow, or advanced plugins (not free) some people spend year or more making to get you started quickly, but Blender also has a lot and many are free wihout needing to buy a plugin (for example animatiosn edit and creation, modeling in game engine and so on).
About visibility, you can make collections , and you can hide all collections you want and only show the collection that has the mode you are working on.
About keeping models on their own Blender file stay away from GPL, this is where you have to use import export and this is the annoying feature making the workflow similar to other 3D engines.
What is missing in the “Save as” in Blender, would be “Only selected”, this would make working with blender files so much smooth without needing to use import export.