The issue is other factors may force you to use an alternate store. My college uses Proctorio for online test-taking. I am required to use this for the class. The issue is, the extension is only available for Chrome (I've tried other Chromium browsers and those don't seem to work as well). As a Firefox user, I don't really like having to switch to Chrome just to use an app that I never wanted to use but am forced to.
The same could apply with app stores—if a company, school, or other requires that you use an app that is only available on a less privacy-friendly or perhaps more intrusive app store, that doesn't sound like an optional/risk-free alternative to me. Once you open the walls there's no going back.
I'm guessing companies that have the resources to go with two separate development teams for each platform will tend to go for that route since it leads to better performing applications. e.g. FB Messenger's blog post about going back to native after using React Native.