It's because apple pushed towards apps and didn't want web apps on their phone. Likely due to the profits they can gain from appstore sales
Native apps would be the better platform in my eyes if the Operating Systems would be better in terms of letting a user manage what a native app have access to and can do.
But currently they are preferred by companies despite more dev effort because they can get more user data without the user having easy ways to prevent that. And of course showing ads without the user being easily able to block them
You're not wrong at all, but it's interesting that iOS launched with only web app support for third party software, and it took community pressure to persuade them to support native apps. There was not even an app store to begin with.
There's nothing technical stopping us from investigating and modifying the apps we install - at least on operating systems that allow you to install unapproved apps. YouTube Vanced only got in legal trouble for distributing a copyrighted work (the YouTube app) which led to ReVanced which is a patcher that doesn't include a copy of the original app.