I don’t think we have a solid source, but there is reason to suspect that Safari web apps were just a stopgap measure. Perhaps Steve’s original vision was apps only through Safari, but, by June 2007, they had probably already done an about-face internally. I highly doubt Apple was able to get its internal APIs into public beta shape between June 2007 and February 2008 (especially given that they had the final push to release Leopard during that same period of time). Work on preparing the APIs for public consumption almost certainly began before June 2007. It could have begun as late as January 2007, I suppose, but I suspect it began at least a year before the launch of the 1st gen iPhone.
The iPad had an SDK in public beta form from Day 1, but that’s a rarity for Apple. Apple usually restrains early app development, and not just on mobile devices. Software development for the Lisa was complicated business involving a debugger Lisa booted into the programmer’s environment OS and another Lisa running the actual software. Early Mac development used the same pattern, it wasn’t until around the release of the Macintosh II that development could be done on device. Early Mac OS X development had some moments of odd APIs and functionality not available through public APIs. The kernel API changed with each release at least until Tiger. Menu Bar items? Weren’t even a thing, you had applets that lived in the dock. These docklets, as they were known, were a private API. In 10.1, Apple removed that API and created the first menu items on Mac OS X using another private API (these apps lived in the memory address of a system process). Third party devs used the API, but Apple blocked them and introduced the public NSStatusItem class. But, until around 10.12 or 10.13, NSStatusItem icons couldn’t be re-arranged like the private API items could.
The iPod and Apple TV began with very limited approaches to additional software. The iPod had games from third parties that went through a tough approval process, and the Apple TV’s apps were distributed with it.
The closest comparison to the iPhone is probably the Apple Watch. Apple clearly was worried about the battery life impact of native watch apps, so, for the first OS release (first year or so of SDK availability, first four or five months of device availability), apps ran as an extension on the phone. Even then, concerns over battery life led to Apple Watch apps being throttled until Apple could develop next gen power management for the Watch.
As a general rule of thumb, Apple won’t release a product until the hardware is 90% of the way there (the 10% is for future headroom, they didn’t let 3G delay the OG iPhone for a year) and the software is 75% of the way there (part of that is future headroom, but part of it is knowledge that real world usage will direct software development, and part of it is avoiding letting software hold back the release of hardware). Early in the iPhone OS 2 days, there was an attempt by third party devs to add copy+paste to their apps, but it stopped working in iPhone OS 2.1 or 2.2 because the way they implemented it ran afoul of app sandboxing. Yes, the App Store was considered so important that Apple released iPhone OS 2 before the app sandbox was finished being implemented.