Firstly I want to say that as a user I hate using the Mac App Store - mainly for all the reasons posted there.
There is one large benefit which is often forgotten. When I use the App Store I don't need to worry about your website/database getting hacked or leaking my personal data/credit card information. This is mostly avoided by indie developers using Stripe or some other popular payment gateway, but it is still a concern and annoyance that is removed by something like the App Store.
That's one of two reasons that I don't mind purchasing on the App Store - the other is licensing.
On the App Store, each app I purchase is licensed for 5 macOS devices and I can unlicense a device/reset the count at any time with a few clicks.
Licensing for other applications is ¯\_(ツ)_/¯ - sometimes it's a single machine, other times X devices, and other times unlimited devices for a single user/owner. And if the 3rd party licensing server is down, I can't activate my purchased applications - I've literally had this happen before. Purchase Paw from their website, licensing was down, I ended up re-purchasing it on the Mac App Store.
And in the future, if they go out of business and the application needs to be activated with an online server, I'm fucked. If I purchase it from the App Store, I'm fairly confident I'm good to go for the foreseeable future.
So many apps still communicate with APIs over the Internet. You might not have to worry as much about specific kinds of attacks like cross site scripting but the attack surface is still present.
There is one large benefit which is often forgotten. When I use the App Store I don't need to worry about your website/database getting hacked or leaking my personal data/credit card information. This is mostly avoided by indie developers using Stripe or some other popular payment gateway, but it is still a concern and annoyance that is removed by something like the App Store.