No, it doesn't. That it's do-able is the point. You can directly go to the hardware and still have it work across the board on all Amigas. There's a lot of API-based software that no longer works on modern PCs. See my other post.
By your own (flawed) reasoning the fact that API-based software still does work on modern PC's demonstrates that it is doable, and thus proves that API based systems are the way forward.
You're trying to have your cake and eat it. Hardware banging, in the modern age, is for embedded projects and the like. it has _no_ place whatsoever on modern desktop machines except for the implementation of hardware drivers.
Recent GPU's have billions of transistors crammed onto their dies dedicated to the job at hand. How far do you think they would actually have gotten if they had to waste precious silicon to appease people that insist on total hardware backwards compatibility with 20-year old designs? Apply the same observation to every other component in your machine.
As for not being able to run old software thanks to hardware changes, I take it you forgot about features like hardware virtualisation or even emulation? After all, there's not much you could do in DOS on a 286 that you couldn't comfortably emulate today if you really wanted to.
Hardware banging and ignoring the OS was never truly encouraged on the Amiga (at least by the people that designed the hardware and software), you are lucky that anything worked from ECS to AGA. And, given that post AGA was set to go in wildly different directions, you'd be even luckier if anything worked beyond that.
You can assume all sorts of utterly ridiculous nonsense if, as an application developer, you view your machine as hardware up rather than software down. For example, the VBR on the 68000 was at a fixed location starting at address 0. From your standpoint, it's t thus perfectly fine when taking over the machine to put your own handlers in that first 1K of memory. And some obviously did, which is why when 68010+ based systems started appearing and the OS got the opportunity to relocate the VBR to somewhere helpful, like fast ram, their code failed miserably. And that's just from "hardware banging" the CPU, let alone assuming other facets of the system architecture would never change.
Frankly I'm glad that not too many people thought your way about development or there's no way we'd ever be using 68060, RTG or AHI. You might find it comfortable in 68000/OCS-only land, but don't assume everybody else did.