You need a native program to access the web, so for now, always you'll need at least one native program ;)
Now, seriously, as muzani states indirectly, the preferred way will be divided as long as implies another layer and a difference in available device services. Also, you mentioned a disadvantage of the stores but think about the distribution network in terms of online presence to being noticed. There're plenty of pros and cons in every aspect.
Regarding the update point, like in desktop OS, with Android, you didn't need to wait, just take the APK file and install it. From the perspective of your sentence, it's only a problem (or situation) of the Apple ecosystem, not related to the web/native. They can't control the web but if they could they will. From the perspective of the consumer, some say they are fine with the gatekeeper, adding a layer of security and quality assurance.
Now, seriously, as muzani states indirectly, the preferred way will be divided as long as implies another layer and a difference in available device services. Also, you mentioned a disadvantage of the stores but think about the distribution network in terms of online presence to being noticed. There're plenty of pros and cons in every aspect.
Regarding the update point, like in desktop OS, with Android, you didn't need to wait, just take the APK file and install it. From the perspective of your sentence, it's only a problem (or situation) of the Apple ecosystem, not related to the web/native. They can't control the web but if they could they will. From the perspective of the consumer, some say they are fine with the gatekeeper, adding a layer of security and quality assurance.