If I'm using the App Store stuff, then my text editor can't edit all my files, my video player can't open videos when I double-click them, my Evernote can't print to PDF, my disk usage analyzer can't analyze my disk because it can't ask me for authorization to do so, and so on.
At the same time, though, in theory I do want sandboxing, at least by default. I do want to have to explicitly authorize some random app before it can install a printer system extension, or before it can scan my entire disk.
I feel like the problem is more political/cultural: Apple prioritizes their low-information, low-computer-literacy users (hi, Dad!) so dearly, that they aren't willing to expend resources to find any compromise for their technically proficient ones. And through the sandboxing requirements, they force their third-party developers to either tell their power users to fuck off, or to give up on the App Store.
Or, I don't know, perhaps they just don't have enough engineers left for the Mac after moving so many of them to their higher-volume Candy Crush console business.
Regardless, though, if there were mechanisms for the user to control the sandboxing enforcement to a greater degree, I would be all for it.
If we could tell our Macs "yes, dude, I hereby authorize DaisyDisk to see all the files" and "Computer, hey bud do me a favor, overrule this restriction that says CotEditor can't ask me to authorize modifying root-owned files", then I would actually not only be happy with, but even prefer, the App Store versions.
But we can't, and it's sad.