if your app needs to access those things/areas, then the plist that accompanies your app needs to include a reason why.
App wrapper will take what you type here and amend the plist for you.
You can leave them blank, as with many many other aspects of App Wrapper.
App Wrapper is all about helping to deal with all the hoops we have to jump through to get an app to work with Macs.
It can set/change things like whether your app supports dark mode and hi-dpi screens.
It can insert icons for you, check your certificates (as you have seen)
The scripting part means you could get it to build your package at the end of a compile process (I choose not to do that, personally)
I made a bug report years ago abour the Finder Rename feature (Rename with an index number) etc. OS versions goes on and the bugs are still there. I know how to work-around some, but it is boring to make two of-r three rename to get the result you’re expected for the first one.