That's what sandbox is for.Any software that runs on a system with untested software is compromised. If you are just running a game or something, that is no big deal. If you are running software that has a security component, it is a big deal. In a corporate environment, you go a step father and only allow software from a very small list. Better yet, you don't allow the user to install their own software at all. IT automatically uploads and updates the software that runs on your device. Each update to an app is examined before it is sent out to users. People can run whatever software they want on their own devices, but they can't touch the company network and quite often, they can't bring their own devices into the building.
Going back to home users, software from third party stores tends to be unreliable at best or trash at worst. If their software is compromising the OS, it will likely make your software look bad. Why deal with bugs that are brought into the system by "Developers" that can't even follow the platform's guidelines?
You don't believe in Apple's own security then?
With this mentality it's not about sideloading but about 3rd party software in general.
And keep in mind - sideloading is optional. You don't want to sideload? Fine! Nothing changes for you. Just continue using App Store as majority of users would. Do I want to trust something other than App Store? My choice, my responsibility. Hell, sideloaded software may be even safer than App Store's one. Why? I can compile open source code and sideload it and so it will be code I can review and trust. Same can't be said about App Store - there have been many cases of fraudulent and sketchy apps there.
You can sideload even today - but you need developer's account for 99 USD per year. More money to the Apple today. With free sideloading, everyone is basically developer for free. So nothing changes from the security standpoint.
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