I have folders set up in BTT based on specific categories (for instance –– all shortcuts with the Fn key, all shortcuts with a Hyperkey, etc.) However, some of these shortcuts are app specific. It seems that there is no way to have app specific shortcuts nestled in folders; they go to a separate place that is accessible from the left sidebar menu. Another issue is that they also don't come up when you navigate to the All Configured Triggers overview; you have to switch over from "All Apps" to the specific app group to see them.
I think it would be neater and more useful to have all of the different triggers organized in one place, and have an option on each trigger to select if it should be attached to all apps, a specific app, or else excluded from app. Being able to see all your triggers at once would make things easier to manage.
It would also be a more elegant solution to the situation where you want to exclude a global trigger from firing in a specific app; right now it seems that the work around is to go to the app you want to exclude, duplicate the trigger, and set the action to "Use Apple default or nothing".
In addition, this means that it would be more straightforward to attach a single trigger to multiple specific apps. For instance, I have a shortcut that automatically selects and copies the URL of the page I'm on. I want this to work in Safari and Chrome specifically, and nowhere else. I have to make two separate shortcuts that are independent from one another. If I want to change it down the line, I have to go and change both.
I know there was a big UI overhaul not too long ago, but hopefully something like this wouldn't be too drastic of a change. Maybe there could be little app icons/names next to the trigger action/note indicating that a certain trigger is app–specific in a particular kind of way.
sorry, the mapping between apps, triggers and actions is one of most fundamental concepts in BTT and I won‘t be able to change this. It’s just the only mental model that makes sense to me and the whole internal data model is made for this setup 
However some of your issues you can easily workaround using conditional activation groups (e.g. create a group for Safari and Chrome, so you only need to create the shortcut once)
One thing that I might add in the future is a „full overview“ that would allow to see all triggers grouped by apps
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I figured as much, since the mapping you mentioned seems pretty central 
Thanks for pointing out the conditional activation groups, I'll definitely explore that!