You must be using a very narrow definition of "hardware architecture". In the 68K era Apple used to custom-design pretty much everything interesting in the box except the processor and memory. The IIfx was perhaps the most extreme example (several custom ASICs and two 6502-based I/O coprocessors, IIRC). For the Newton we even designed parts of the processor (e.g., the MMU).
Let's take your example of the IIfx: off the shelf 68k processor on NuBus. ASICs and I/O coprocessors are just devices. Granted I didn't know about the custom processor work on the Newton, but if IIfx counts as a new hardware architecture, then so does the x86 move from ISA and 8259A to PCI-E and APIC. And I don't think it makes sense to argue that today's Macs have anything resembling a custom architecture.
Symbolics' systems and the first AS/400 models (the last new hardware/software architecture developed by IBM) are in a totally different class.