> Free native apps abound.
Yes? I haven't claimed there aren't free native apps.
> Web apps tied to subscriptions are also plentiful.
Fair, but most of the ones I know are usually technical apps or they offer something else that is not about software (for instance, storage more than the app).
> the web is unique in allowing you to actually inspect the source that is running on your machine
That is not unique, nor true.
Uniqueness: you have apps made in scripting languages everywhere. Even for compiled languages it is a decision not to give you the code, not a technical one.
Truthness: many webs are obfuscated on purpose like native apps are.
> you have no way of verifying that the code in an open source repo is what actually runs inside your iOS app.
False, you can definitely verify that a binary matches the source code in deterministic builds and even provide debugging symbols etc. The fact that many projects don't care about that does not mean there is "no way", it just means the overwhelming majority of users do not care.